There are several programs that allow an MS-DOS system to work with an
Atari-format 5.25" diskette.  Each of these work with the Atari SS/DD 180K
format, so you'll need an Atari DOS and disk drive capable of this format. 

#1 Choice:
Atari-Link PC (AtariDsk) V1.2 (c) 95-12-09 by HiassofT (Matthias Reichl)
Ataridsk is a program for MSDOS-PCs that allows you to access Atari floppy
disks in double density (180k). All you need is a PC (XT or 286 should be
sufficient) and a 5.25" floppy drive. Features of this tool:
    * Menu driven user interface
    * read, write and format Atari disks on the PC
    * small size (only 35k)
http://www.horus.com/~hias/atari/

Also by HiassofT (Matthias Reichl):
  WriteAtr V0.92b
  With WriteAtr you can write double density ATR-images to Atari floppy disks
  on your MSDOS-PC. You can also create ATR-images of double density floppy
  disks! All you need is a PC and a 5.25" and/or a 3.5" floppy drive.
  Version 0.92b added experimental support for the enhanced density (1040
  sectors/128 bytes per sector) format. Please note: this format doesn't work
  with a lot of floppy controllers - use it at your own risk!
  http://www.horus.com/~hias/atari/

#2 Choice:
MyUTIL by Mark K Vallevand.  Based on Charles Marslett's UTIL.
  http://www.umich.edu/~archive/atari/8bit/Diskutils/Transfer/myutil.zip
  Includes SpartaDOS disk utility v0.1e to access 180K SpartaDOS disks

Other similar utilities:
ATARIO by Dave Brandman w/ Kevin White - Reads SS/DD 180K Atari disks.
  www.umich.edu/~archive/atari/8bit/Unverified/Diskutils-redist/atario21.arc
SpartaRead by Oscar Fowler - Reads SS/DD 180K SpartaDOS disks.
  http://www.umich.edu/~archive/atari/8bit/Diskutils/Transfer/sr.arc
UTIL by Charles Marslett - Reads/Writes SS/DD 180K Atari disks.
  http://www.wordmark.org/

Here's some advice on using the above utilities from Hans Breitenlohner:

There are two technical obstacles to interchanging disks between
DD Atari drives and PC drives.

1. The Atari drive spins slightly slower (288 rpm instead of 300 rpm).
   If you format a disk on the Atari, then write sectors on the PC, it is
   possible that the header of the next physical sector will be overwritten,
   making that sector unreadable.  (The next physical sector is usually
   the current logical sector+2).  The solution to this is to format all
   disks on the PC.
       (Aside:  Does anybody know how this problem is handled on the
        XF551?  Is it also slowed down?)
     Konrad Kokoszkiewicz answers:
     "The XF551 disk drive is not slowed down - these drives are spinning
     300 rotations per minute. To prevent troubles with read/write disks
     formatted and written on normal Atari drives (288 rot/min), the main
     crystal frequency for the floppy disk controller is 8.333 MHz
     (not 8 MHz, as in 1050, for example)."

2. If the PC drive is a 1.2M drive there is the additional problem of the
   track width.
   The following is generally true in the PC world:
    - disks written on 360k drives can be read on either drive
    - blank disk formatted and written on 1.2M drives can be read on
      either kind
    - disks written on a 360k drive, and overwritten on a 1.2M drive,
      can be read reliably only on a 1.2M drive.
    - disks previously formatted on a 360k drive, or formatted as 1.2MB,
      and then reformatted on a 1.2M drive to 360k, can be read reliably
      only on a 1.2M drive.
    (all this assumes you are using DD media, not HD).

   Solution: Use a 360k drive if you can.  If not, format disks on the
   Atari for Atari to PC transfers, format truly blank disks on the PC
   for PC to Atari transfers.

Jon D. Melbo sums it up this way:
   So a basic rule of thumb when sharing 360KB floppies among 360KB &
   1.2MB drives is: Never do any writes with a 1.2MB drive to a disk that
   has been previously written to in a 360KB drive....UNLESS... you only
   plan on ever using that disk in the 1.2Mb drive from then on out. Of
   course a disk can be reformatted in a particular drive any time for use
   in that drive.   As long as you follow that rule, you can utilize the
   backwards compatible 360KB modes that most 1.2MB drives offer.

While the above mentioned utilities work with SS/DD 180K Atari-format disks or
SS/DD 180K SpartaDOS disks, the following combination of utilities has been
used successfully to read SS/SD 90K Atari-format disks.  So if you only have
standard Atari 810 and/or Atari 1050 drives, you could look into:

AnaDisk -- now a product of New Technoligies Inc. (NTI)
See: http://www.forensics-intl.com/anadisk.html
The current version is "not made available to the general public" (!)
Previously a product of Chuck Guzis @ Sydex, http://www.sydex.com/
Older versions available: http://ch.twi.tudelft.nl/~sidney/atari/
- Reads/Writes "any" 5.25" diskette

DeAna by Nate Monson
Available: http://ch.twi.tudelft.nl/~sidney/atari/
- converts AnaDisk dump files from Atari format

See http://ch.twi.tudelft.nl/~sidney/atari/ for tips on using this
combination of utilities.

Preston Crow writes:
  "As best as I can figure it out, if your PC drive happens to read
  FM disks (I'm not sure what the criteria for that is), then you
  can read single density disks on your PC by dumping the contents
  to a file with AnaDisk, and then using Deana.com to convert the
  dump file into a usable format.

  For enhanced density disks, Anadisk generally only reads the first
  portion of each sector, but it demonstrates that it is possible for
  a PC drive to read enhanced density disks."