The sport package also has 4:11 gears, bigger brakes, and stiffer sway bars. My wife's '01 Sport rides nicer than my Avalon.
Things I noticed when I bought hers (used):
Don't be too worried about grease slung everywhere underneath. It's a sign that the oil was changed at a shop that knew to grease the driveshafts. If done regularly, there will be grease slung around in the vicinity of the u-joints.
Don't be too concerned about oil buildup on top of the skid plates. The oil filter is accessed through the drivers fender well (the rubber skirt might be missing or loose just to the front of the spring) and when changed in this fashion, you cannot help but lose a cup of oil onto the top of the skid plates. After learning this the first oil change, I started removing the skid plates to change the filter. Takes extra time, but is better than oil spots on the driveway IMO. If you off road, it gives you a chance to pound the dents out too ;-)
The power antenna's had failed on about half of the 4Runners I looked at (in WI, maybe the winters have something to do with it). Her's still works, but needs WD40 regularly.
The fiberglass shroud under the drivers side floorboard was broken on about half of the trucks I looked at, some probably from off roading, and some probably from being on a lift. Again, no big deal.
You can easily check the VIN stickers on every major body part to see if it has been crashed and had parts replaced. They are little silver Toyota stickers on the hood, fenders, doors, hatch, etc, and should all match each other. They cannot be removed without being destroyed, so replacement parts will not have matching stickers. Not that a crashed truck cannot be put back together to a high level of quality, but you should know what you are getting.
If you think the jack is missing, it's under the rear seat, not in the removable panel at the rear like a lot of other SUV's.
Lastly, because of all the hurricanes the last few years, I spent time underneath every truck I drove, sticking my fingers in holes in the frame looking for any sign of mud from flood damage.
These trucks are known for reliability, and as far as I know, there really isn't a history of any common parts failures. As the other poster mentioned, they make a lot of "whirring" & "clicking" sounds, especially right after start up. They all do this, and I think the owners manual even makes mention of it.
Hope this helps. Ours replaced a Chevy Blazer, which replaced a Jeep Cherokee, and I don't think I will ever buy any other than Toyota from here on out.
Scott