Hey, welcome back! Another vehicle quest, huh? What is this, like Toyota no. 9 or something for you?
99-00 are the most desirable for a couple of reasons. First of all, the 96-98 models (which are identifiable by their lack of the "fat lip" energy absorbing bumper) generally had a lower suspension and the interior driver/passenger area is not nearly as nice (terrible cup holders and only one power outlet in the front being the biggest complaints.)
The 1999 facelift gave the 4runner the better interior and features like auto up/down front windows (both of them), headlights that turn off automatically if you leave them on, a way to store the rear seat headrests when you fold the seat down and a few other creature comforts. My 99 also had the rear passenger heater (this is actually a separate heating unit with the fan under the passenger seat and a set of controls for the rear seat passenger.)
1999 models are also known as the "tall coil" models because they had the tallest suspension. Here's a picture of my '99 with bone-stock suspension running 265/75/16s (just one size up from the factory tire size of 265/70/16):
Keep in mind this photo is from 2010 so the suspension had had 11 years to sag by this point and it's still pretty tall.
Another plus for the 99-00 models is that the limited version (which was auto-only) had a multi-mode transfer case that allowed you to run in 4wd on dry pavement if you wanted to, or to run in 2wd, or to lock the center diff. Most Limiteds also had the rear E-locker. The 99-00 limiteds and the 2009 Trail Edition were the only 4runners that ever had BOTH multi-mode AND a factory rear E-locker. Even the modern 4runners don't offer this option (on the modern 4runners you can get an E-locker with conventional 4wd on the TE, but there's no multi-mode option.)
If you want a 4 cyl, 2000 was the last year for that option and also the last year a manual tranny was available. The Highlander/Sport Edition (with the hood scoop) seems to be the most desirable 3rd gen out there, bonus points if it has a 5 speed.
A final plus for the 99-00 models is that they didn't have the problematic traction control system that the 2001-2002 models did (you'll see this as a common topic over on T4R.org.) All 4wd 2001-2002 4runners had multi-mode 4wd and they were all 3.4/autos.
Downsides to the 3rd gen include a very unreliable fuel gauge and a fuel tank that IMO is terribly undersized (18.5 gallons.) Combined with lackluster MPG this results in a cruising range of less than 350 miles on the highway (in practical terms, you'd be looking for a gas station before 300) and in the city, a practical range of a little over 200 miles. If you go over to the T4R.org 3rd gen forums, you will find that MPG and range complaints are the biggest ones there.
Other thing to watch out for with the auto is the dreaded "pink milkshake" tranny failure caused by a failure of the radiator-mounted tranny cooler that lets antifreeze mix with the transmission fluid. The good news is that you can mount an aftermarket tranny cooler and bypass the factory cooler entirely which prevents this problem.
I liked my 3rd gen a lot, off road it was tremendously capable. If I didn't need to pull a trailer, I would probably still have it. However, the lack of power to pull even a small trailer like Bubbles as well as the short range (which caused us to run out of gas in Oregon last year) made me trade it in for a 4th gen, and while the 4th gen is not as capable off-road, it's much better as a tow vehicle. It's also better in marginal weather because of the multi-mode 4wd that all 4th gen V6 4wd models came with.
Hope that helps!
