Much as I like my 3rd gen (and I do) I think they're way overpriced in the used market. There's no rational reason that a 1999 4runner with 125k on it sells for $8k and an equivalent Montero or Trooper sells for less than half that.
OTOH, the nice thing about them is that even at 10 years on (the newest 3rd gen is approaching 10 years and the oldest is approaching 17) there are no real "known failure points." The 3.4 engine is rock solid, kind of the 22r for the 21st century (i.e. not a powerhouse but will last forever.) The auto trannies are subject to failure but usually that failure occurs at the radiator when radiator coolant mixes with tranny fluid from the factory tranny cooler. Easy to prevent for <$100 with an external cooler. The IFS is relatively easy to lift (compared to a T-bar equipped vehicle) and the aftermarket support is decent, although not anywhere near what you have with the Jeep!
If you're set on a Toyota, that's fine but do yourself a favor and at least give a look at the competitors. I, personally, don't like paying more for things than I have to and the "Toyota Tax" is a little high for me.
It's crazy when you think that in some cases you can get a 2nd gen Xterra (2005 - up) for just a little more than people are asking for a 3rd gen 4runner (I've seen 2nd gen X's offered for $14k and 3rd gen 4runners offered for as much as $15 or $16k if they have low miles. Crazy!)
EDITED TO ADD: As nice as they are, 3rd gens do have a few negatives and there are other "good to know" things about 3rd gens.
* Fuel gauges are notoriosly inaccurate. Some will show you with 1/4 tank when you're bone dry, others (like mine) show you below E when there's still 1/4 tank left.
* The factory 18.5 gallon tank is, IMO, marginal in terms of size because the MPG (especially with the automatic) isn't that great. If you keep a light foot on the throttle, you can squeeze 300 miles out but 220-240 is more reasonable (by contrast, my '90 Montero had a 24 gallon tank that gave it a 400 mile range, which I consider to be much more appropriate for an off-road vehicle.)
* The Limited models from 99 - up have a fancy digital HVAC control. When it works, it's great. When it doesn't, it's very expensive to replace (Toyota wants >$1k for the piece.) I think some people have tried refitting manual HVAC controls but I don't know if that works. Check Yotatech or t4r.org.
* The 3rd gen underwent a major facelift for the 1999 model year. These trucks are easily identifiable by the "Fat lip" energy absorbing bumper. They are generally considered more desirable which is why the 96-98 models can often be found cheaper. Along with the facelift came some interior mods like better cup holders, multiple power points in the dash, auto up/down on both front windows, and headlights that turn off automatically if you leave them on and then remove the key and open the door.
