Since I've owned it: leaks at valve cover gasket, oil pan gasket, exhaust manifold gasket. Sticky throttle body cable, hole in muffler. Rusted rear window carriers inside the tailgate.
In 2001 the engine overheated for the previous owner while towing, resulting in an engine fire and a total rebuild of the 22RE motor.
My most recent 4Runner is a 1995 4-cylinder 22RE, originally from Nevada, so rust is minimal. It was brought to BC in 2003. Now, in 2015, it has no body or frame rust and runs great! With any 20 year-old car, I expect a bit of wear, but there isn't much. It starts every time and goes places I'd never expect a stock 4Runner to go (up mountains and through water, over rocks, climbing hills, etc). It is an amazing 4x4! I've given it a complete tune-up and I make sure I give it regular oil changes. Back window works, heat works.
It starts every time, has taken me on many road trips, and is great on gas, being a 4 cylinder. Even the battery is 6 years old, but it never fails. It might not win any races, but I don't drive fast anyway.
My last 4Runner was a '91 V6; I bought it at 300,000 km (186,000 miles) and I never had any problem in the 2.5 years I owned it, except for ball joint replacements, a few oil leaks, and expected wear and tear of brakes, shocks, and tires over time. It was a 3.0 gas guzzler, so I ended up letting it go in search of a 22RE. I'm so glad I did!!!