According to Chips Yap <chips2@pc.jaring.my>:

"For those interested (and many of you might be as you'd have a new
RAV4), these are some of the things I do when I run-in a new vehicle. 
The process is usually useful for the first 5,000 kms or 3,500 miles.
(Disclaimer: If you choose to follow any of the tips here, I accept
no responsibility for any damage or loss resulting).

First of all, why run-in a new vehicle? The reason is that the 
manufacturing process of metal parts leaves them with some minute 
imperfections and also they are being mated against other parts. 
Running-in enables these parts to interface more smoothly by causing 
a certain degree of beneficial wear and also by wearing down the 
imperfections. Note that they aren't defects in any sense. A visible 
example would be on new tires where you see stuff that looks 
like 'hair' sticking out. As you drive around, they get worn off.

Over the past decade, manufacturing processes have improved a lot and
the parts are coming out more perfect in form and tolerances are finer.
So the running-in process is not as crucial - but still important - as
before when you even had to use special oil which permitted a higher 
wear rate.

New engines are tight because everything's new so some degree of wear 
has to occur to allow them to rev freely. But unlike a decade or two 
ago, you don't have to be as 'religious' about running-in and I note 
that the manuals are now providing only basic and simple advice. In 
fact, the notion of treating a new engine with tender loving care 
contrasts to what you will find if you visit an engine factory. The 
new engines, after assembly but before installation in the car, are 
run at high revs by a computer. It provides some running-in and also 
allows for checking of integrity or whatever. But to see it being 
done can be quite shocking!

You still need to run-in a new car and engine, allow the various parts 
to bed in and function with each other efficiently.  This calls for 
thoughtful driving strategies but they are not necessarily boring. 
The main thing to remember is not to allow your engine to load up, 
meaning you don't try to drive it up an incline in top gear and 
labor the engine. The load is bad for the engine at any time, more 
so when it's brand new.  The effects can be long-lasting and ruin the 
engine's ability to give its best for the rest of its life.

Even if you have an autobox, it's a good idea to manually disengage
the overdrive on an incline or even slot into 2nd. You won't hurt the 
engine by doing that and you will even do it a favor if you help it to 
run up the incline with less effort. Using the gearbox, auto or manual, 
liberally is a good way to run it in and you will be rewarded by a 
smoother unit later on.

Varying the speed is also an important point and it is mentioned in 
the manual. This exercise is intended to get your engine used to high 
and low revving conditions. If you have cruise control, don't use it 
for at least 3,500 miles because the constant speed is not good. Even 
on the highway, you should vary your speed a lot. You can do so as you 
drive by using lower gears and shifting up and down.

But you should also pay attention to what rpm you run up to. For the 
first few 100 miles, maybe you shouldn't get past 4000 rpm. Then you 
can gradually go higher and by maybe 1500 miles, you can start to push 
it to 5000 rpm. Do not run it up to 5000 rpm and just hold it there; 
rev it up as you're driving and change up quickly when you get to 
5000 rpm.

When you get up to 2000 miles or more, maybe you might like to try
running it up to the redline for brief spurts. I learnt that this is 
helpful for the engine from a racing driver and mechanic. You 
accelerate in 2nd gear up the the redline and shift up right away. 
Don't hold it there longer than a shift action. Why? The high revs 
give the engine a 'taste' of that sort of condition and prepares it 
for the ability to cope with such conditions. It's like when you do 
a high-speed run down the highway and after that, the engine feels 
nice and free-revving (although that's more of the oil being well 
circulated too).

If you stick to low revs all the time, there is a possibility that your 
engine will remain tight and unwilling to give all its potential when 
you want to drive hard and fast. I have experienced engines where 
the owners really pussy-footed them in the run-in period and they 
never had an edge in performance compared to other similar engines.

The manual doesn't seem to recommend an oil change at 1000 km (600 mi) 
but I am used to it and will do so. No harm and the only thing that 
will be hurt is my pocket. I personally believe that the first 600 
miles are a time of great wear inside and so the oil will have a lot of 
metal stuff in it. The filter will remove it, of course, but it's still 
there and it's minute too. I'd rather get rid of the dirty oil and have 
some new oil inside; besides, the original oil is of unknown quality 
to me although I'm sure Toyota would use something good enough. The 
next oil change would be at 5000 kms or 3500 miles, but you can follow 
the interval indicated in your manual.

For the brakes, I also take a bit of care. You need to brake a lot 
to run-in the new pads but you also have to be cautious about how 
hard you brake. Excessive pressure on new pads can cause them 
to glaze over and that's going to reduce braking power. Some people 
drive around with a very light pressure for a while to wear them 
out a bit but you need to really be deliberate about that.

Other things: I like to use Rain-X, a liquid which makes the glass
very slippery so that water beads off easily. I put it on the front 
and back, the front side windows and the door mirrors. It's 
corrosive so don't let it get on your paintwork!

I also like to spray on fabric protector which helps to stop 
moisture from seeping in (most of the time).

And I've earlier mentioned the point about loose screws and bolts. 
Take a screwdriver and small spanner (preferably a box type) and 
gently tighten the fasterners you can see. Not too tight but if you 
find them able to take another turn, then do so. From experience, 
I've always found the bolts holding the front fenders to the body 
(along the side of the engine bay) to be less than tight (same thing 
in the RAV4)."