Some quick definitions first:

NTSC: "National Television Standards Committee"
TV signal standard used in North America, Central America, a number of South
American countries, and some Asian countries, including Japan.
  o  525 lines per frame
  o  60 half-frames per second (interlaced) = 60 Hz
  o  Complete frame refreshed 30 times per second

PAL: "Phase Alternation by Line"
TV signal standard used in the United Kingdom, most of the rest of Europe,
several South American countries, some Middle East and Asian countries,
several African countries, Australia, New Zealand, and other Pacific island
countries.
  o  625 lines per frame
  o  50 half-frames per second (interlaced) = 50 Hz
  o  Complete frame refreshed 25 times per second.

SECAM: "Sequentiel couleur avec memoire"
TV signal standard still used in France, the former USSR, and some African
countries.  Until the 1980's SECAM was the standard in eastern Europe,
including East Germany, Poland, Czech Republic, Slovakia, and Hungary.
  o  625 lines per frame
  o  50 half-frames per second (interlaced) = 50 Hz
  o  Complete frame refreshed 25 times per second.

While the above draws a clear distinction between NTSC and PAL/SECAM, a
further discussion of the NTSC/PAL/SECAM color encoding systems will help to
distinguish between all three standards.

=-=-=-=-=
This discussion by Laurent Delsarte (2008.12) (with minor edits by mc).

First of all, it is important to remind that NTSC, PAL and SECAM are all
color encoding systems.  They are used in conjunction with older standards
for the base monochrome signals--the old standards that were used when all
the TV sets were still black & white.

In other words, the first televisions standards, referenced with letters
(M/B/G/I/K/etc.), were used to broadcast pure monochrome, black & white
images.  The NTSC, PAL and SECAM standards were then introduced to add a
specific color signal to colorize this pure monochrome signal.

When the color was introduced, the idea was to remain compatible with the
existing old black & white TV sets, so that these old black & white TV sets
would still continue to be able to display the image (but in black & white,
obviously).

In the television world, the black & white image, also known as the
monochrome signal, is called the "luminance" ("Y" for short); whilst the
color information is called the "chrominance" ("C" for short).

For every dot defining the image, the "luminance" states how intense
(ranging from pure black to pure white) the dot is.  For every dot defining
the image, the "chrominance" states what is the color of the dot (within
the limit of the color palette that the color standard allows).

In the Atari 8-Bit world, the "luminance" notion can be understood if you
use the standard Graphics mode 9: you have just one color at your disposal
(say, white), and all you can do is draw graphics using 16 intensities of
white (ranging from pure black to pure white).  And the "chrominance" notion
can be understood if you use the standard Graphics mode 11: you have 16
colors at your disposal, but they all have the same intensity.  You control
the color, but not the brightness of the color.

To display a black & white image, the "luminance" ("Y") signal is enough.
To display a color image, the "luminance" ("Y") and the "chrominance"
("C") signals are needed.  When a black & white TV set receives a color
signal, it uses the "Y" signal as usual and remains unaware of the existence
of the "C" signal.  When a color TV set receives the same color signal, it
processes both "Y" & "C".

In practice, the chrominance ("C") is transmitted with two separate
signals, "U" and "V". Now you probably recognize the familiar "YUV" acronym
you've surely seen in discussions related to TV signals.

To simplify, PAL & SECAM signals are quite similar, except that they use a
different way to transmit the "U" & "V" signals ("chrominance").  PAL
transmits "U" & "V" together, then the same "U" & "V" information again but
slightly differently, to increase the accuracy.  SECAM transmits "U" then
"V".

The way that PAL vs. SECAM handle color is thus very different but since the
black & white TV standards were quite similar across Europe (625 lines / 50
Hz), a PAL TV set is very likely to be able to display a SECAM video signal
(and the other way around), but in black & white (because it can decode "Y"
but not "U" nor "V").  
 
The situation is totally different with NTSC vs. PAL.  Although they are very
similar in the way they handle color, they are based on totally different
black & white TV standards (625 lines/50 Hz for PAL, 525 lines/60 Hz for
NTSC).  You have to remember that, by design, the 50 & 60 Hz display refresh
frequencies were based on the mains (household electric power supply)
frequencies: 110v 60Hz in USA and 220-240v 50Hz in Europe.  Up to the mid-80s,
devices that were able to handle both 50 & 60 Hz video signals were very
expensive.

Nowadays (2009), almost any PAL TV set is able to display a 60 Hz NTSC video
signal.

While it often enough to distinguish between NTSC/PAL/SECAM, in practice each
color encoding system has been combined with multiple earlier monochrome
broadcast standards.  Thus, to fully specify the broadcast signal standard
used in any given country, both color system and base monochrome system is
indicated.  Common examples: NTSC M, PAL B/G, SECAM L.  A more complete list:

 NTSC M   : USA
 NTSC J   : Japan
  PAL B/G : Germany, Austria, Belgium, Denmark, Spain, Finland, Netherlands,
            Italy, Norway, Portugal, Sweden, Suisse, Algeria, Turkey, Ghana,
            India, Israel, New-Zealand, Australia, Malaysia, Thailand, etc. 
  PAL I   : United Kingdom, Ireland, Hong Kong. 
  PAL D/K : Romania, China, Burundi, Cameroun, etc. 
  PAL M   : Brazil. 
  PAL N   : Argentina, Uruguay. 
SECAM L/L': France, Monaco 
SECAM B/G : Greece, Iran, Egypt, Saudi Arabia, Libya, Morocco, Tunisia, etc.
SECAM D/K : Bulgaria, C.E.I., DOM TOM, etc.

In France (Europe), in the early 80s, it was possible to buy "SECAM" devices
(TV set, VCR, etc...) or "PAL/SECAM" devices; the latter - being able to
process both SECAM and PAL signals - were more expensive.  For instance,
"PAL/SECAM" TV sets were popular among movies addicts (owning high end
equipment such as PAL LaserDisc players, etc) and for people living close to
a PAL-broadcasting country (at the Belgian border for instance, to receive
the PAL Belgian French-speaking programs).  Last but not least, some
companies did manufacture some PAL-to-RGB "video translators" devices, to
convert a PAL signal into a universal RGB signal, that most SECAM TV sets
were able to accept as video input.  These PAL-to-RGB "video translators"
were quite useful to display PAL signals (from various home computers,
including PAL Atari XL & PAL Commodore 64) on SECAM TV sets.  The models
manufactured by "CGV" (the company still exists, www.cgv.fr) were very
popular and widely available in the computer shops.
(actual pictures available: http://www.atari800xl.eu/public/cgv-pvp80.zip )

Consequently, in 1984, Atari France was not afraid to distribute PAL 600XL
& 800XL computers in a SECAM country (although it could increase the total
cost of the solution).  Indeed, it would have been dangerous to ignore this
market, where other US competitors were already present and successful
(Commodore 64, Apple II, etc).  The French owners of the PAL Atari XL
computers had two choices:
- Use a PAL/SECAM TV set
- Buy a PAL-to-RGB converter, and use a common SECAM TV set
A couple of months later (Q4, 1984), the SECAM Atari 800XL computers were
finally available.

It is worth noting that in the early 80s the Atari 400 and 800 models had
also both been officially distributed in France, but only the PAL models,
and only in specialized computers shops.  Consequently, they were more
difficult to acquire, very expensive and limited to wealthy amateurs.

=-=-=-=-=
Piotr Fusik writes (3/06):
   In Poland we had PAL Ataris, which was a problem in the time
   of SECAM.  You could connect a PAL Atari to a SECAM TV, but there was
   no color and (IIRC) no sound.  The solution was to buy an inexpensive
   converter mounted inside the TV, so the TV supported PAL in addition
   to SECAM.  This was quite popular, because the VCRs were PAL, too.

=-=-=-=-=
In some ways the specifications of the hardware in the 8-bit Atari computer
are closely linked to the specifications of the television signal standard
used in the market where the machine was designed to be used.  Thus there were
different versions of the Atari computers produced for different markets,
based on the TV standards used in those markets:

 NTSC versions: 400,800,1200XL,600XL,800XL,65XE,130XE,XEgs
PAL B versions: 400,800,600XL,800XL,65XE,130XE,800XE,XEgs
PAL I versions: 400,800,600XL,800XL,65XE,130XE,XEgs
SECAM versions: 800XL,130XE,XEgs

NTSC computers contain NTSC versions of the ANTIC and CTIA/GTIA chips;
PAL computers contain PAL versions of the ANTIC and GTIA chips;
SECAM computers contain a PAL version of the ANTIC chip, and the FGTIA chip.

=-=-=-=-=
So with all that out of the way...

What are the software compatibility issues surrounding all these different
NTSC/PAL-B/PAL-I/SECAM versions of the Atari 8-bit computers?

 -- PAL B and PAL I computers differ only in the TV channel frequencies used
by the RF signal produced.  So in terms of sofware compatibility, all PAL
Atari computers are indistinguishable.

 -- The FGTIA is designed to be 100% software compatible with the PAL GTIA.
This fact, along with the fact that SECAM computer models include a PAL ANTIC,
mean that the PAL and SECAM versions of the Atari computers are completely
software compatible, but with one practical exception: in GTIA Graphics Mode 1
(BASIC Graphics mode 9), while the GTIA can display 16 distinct luminances,
the FGTIA can only display 8 distinct luminances.

Thus the situation essentially simplifies down to just two sets of Atari
computers that may have potential software compatibility issues between them: 

NTSC computers vs. PAL/SECAM computers

=-=-=-=-=
What might happen if you run a software program designed with an NTSC Atari on
a PAL or SECAM Atari, or a program designed with a PAL or SECAM Atari on an
NTSC Atari?  There are a number of possibilities:

1) The program may run faster or slower than intended.

In order to work with the different timings of the NTSC and PAL/SECAM video
signal standards, components of the NTSC versions of the Atari computers run
at slightly different speeds than they due on PAL/SECAM Atari computers.

The CPU clock rate of the PAL/SECAM Atari computer is slightly slower than
that of the NTSC Atari:
       NTSC machines: 1.7897725 MHz
  PAL/SECAM machines: 1.7734470 MHz
Software timing that is based exclusively on the CPU clock rate would thus run
nearly 1% faster/slower on the opposite type of Atari.  This effect, while
small, can be significant in applications that are computation- or timing-
sensitive, such as music players, or in any programs designed to simulate real
time.

The screen refresh rate of the PAL/SECAM Atari computer is considerably slower
than that of the NTSC Atari:
       NTSC machines: 59.94 Hz
  PAL/SECAM machines: 49.86 Hz
Software that operates as a Vertical Blank Interrupt (VBI), that is, software
that is repeatedly executed during the times between screen frame refreshes,
is thus executed at considerably different frequencies on NTSC machines vs.
PAL/SECAM machines.  Based on this effect alone, a VBI programmed on an NTSC
machine would run 16.8% slower on PAL/SECAM machines.  Conversely, a VBI
programmed on a PAL/SECAM machine would run 20.2% faster on NTSC machines.
  (59.94Hz-49.86Hz=10.08Hz ; 10.08Hz/59.94Hz=16.8% ; 10.08Hz/49.86Hz=20.2%)
These calculations ignore the above-mentioned CPU clock rate differences,
which would also come into play.

2) The program may exhibit some sort of "screen flickering" effect.

The ANTIC display list is the software program responsible for the video
display, horizontal scan line by horizontal scan line.  There are 262 lines
available in the (non-interlaced) NTSC video signal, while there are 312 lines
available in the (non-interlaced) PAL/SECAM video signal.  If software written
on a PAL/SECAM machine sets up an ANTIC display list that is made up of more
scan lines than are available in the NTSC video standard, the program will
exhibit a "screen flickering" effect if run on the NTSC Atari.

3) The system may crash.

NTSC and PAL/SECAM machines have different numbers of machine cycles available
for execution of software routines designed as vertical blank interrupts
(VBIs). 

An Immediate VBI must complete execution within the number of machine cycles
available during the vertical blank time:

  NTSC: 2508 machine cycles 
    (262 NTSC scanlines - 240 Atari scanlines) * 114 cycles/scanline
  PAL/SECAM: 8208 machine cycles
    (312 PAL/SECAM scanlines - 240 Atari scanlines) * 114 cycles/scanline

  8208 - 2508 = 5700
  PAL/SECAM machines have a total of 5700 more machine cycles available for
  Immediate VBIs than are available on NTSC machines.
  
A Deferred VBI must complete execution within the number of machine cycles
available from one vertical blank to the next.  The number of machine cycles
available for a Deferred VBI depends upon the ANTIC Display List in use, but 
the upper limit may be derived from the total number of machine cycles per
frame:
       NTSC: 29859 machine cycles / frame
  PAL/SECAM: 35568 machine cycles / frame

  35568 - 29859 = 5709
  PAL/SECAM machines could have as many as 5709 more machine cycles available
  for Deferred VBIs than are available on NTSC machines.

If there are not enough machine cycles available on an NTSC machine to execute
a VBI that was developed on a PAL/SECAM machine, the NTSC system will crash.

4) The colors displayed by the program are not what was intended.

When utilizing ANTIC graphics modes 2, 3, or 15, NTSC Atari computers exhibit
unique color artifacting effects that are not present on PAL/SECAM Atari
computers.  (Artifacting is discussed elsewhere in this FAQ list.)  As a
result, software that utilizes one of these high-resolution graphics modes can
appear to be using very different colors on NTSC machines in comparison to
PAL/SECAM machines.

Also, the additional color frequency generation circuitry present in PAL/SECAM
machines produces a color palette that is similar to, though different from,
the color palette of NTSC Atari computers.  These differences are subtle
enough that they are generally not problematic.

5) The program may explicitly refuse to run on incorrect hardware.

Software may be designed to determine whether the Atari is NTSC or PAL/SECAM,
and refuse to run if the hardware present does not match what is expected.

6) The program may not load correctly at all.

This would mostly likely result from copy protection techniques based upon
precise hardware timing associated with disk drives, cassette recorders, or
components of the computer itself, where the timing was not anticipated to
vary depending upon NTSC vs. PAL/SECAM hardware.

According to Jindroush (2/26/02), two examples of programs that run on NTSC
machines but not PAL/SECAM machines as a result of timing-based copy
protection techniques (probably based on vblank timing) are Transylvania and
The Quest, both by Penguin Software.

7) The program may run fine on both NTSC and PAL/SECAM machines.

Either the differences are too slight to matter, or the software may be
sophisticated enough to detect NTSC vs. PAL/SECAM hardware, as described
above, and act accordingly.

An example of a program that alters its behavior depending upon detection of
NTSC versus PAL/SECAM is Ghostbusters by Activision (checks the GTIA type).

=-=-=-=-=-=-=
How can software determine whether it is running on NTSC or PAL/SECAM
hardware?

Several techniques are available to programmers, as follows:

(1) On XL/XE systems (not 400/800 systems), the OS provides a flag called
PALNTS at decimal memory location 98 (hex: $62).  PALNTS indicates whether the
CTIA/GTIA/FGTIA has reported itself to be NTSC or PAL/SECAM, where 0 means
NTSC, or 1 means PAL/SECAM.  In Atari BASIC, enter "? PEEK(98)" to determine
the value of the PALNTS flag.

(2) An approach which works on all 400/800/XL/XE systems is to use the same
method used by the XL/XE OS to set the value of the PALNTS flag described
above.  That is, to read and interpret the "PAL" memory flag, decimal location
53268 (hex: $D014).  The value of PAL is provided by the CTIA/GTIA/FGTIA chip
itself.  Meanings are:
  Bit 1-3 clear (xxxx000x) = PAL/SECAM
  Bit 1-3 set   (xxxx111x) = NTSC
(Proper interpretation of the value returned by PEEK(53268) in Atari BASIC
would thus be a bit of a programming challenge.  This is left to the reader!)

(3) Software may determine NTSC or PAL/SECAM by determining how many scan
lines are being generated by ANTIC.  The NTSC ANTIC generates 262 scan lines,
while the PAL ANTIC generates 312 scan lines.  (This technique is utilized by
the "Numen" demo by Taquart, which refuses to run on an NTSC ANTIC.)

=-=-=-=-=-=-=
Bottom line:

Software written for NTSC machines (North America) will (almost) always work
on PAL/SECAM machines (Europe), but software designed on PAL/SECAM machines
sometimes won't work as intended on NTSC machines.

Replacing the NTSC ANTIC chip in an NTSC Atari with a PAL ANTIC changes the
screen refresh rate to 50Hz, allowing most of the PAL/SECAM-only European
software to run on a North American NTSC Atari.  However, make sure your
display device can support a 50Hz PAL signal first!

North American Atari users might also obtain and use real European PAL or
SECAM Atari machines, with the same caveat concerning the display device.