My driver's window switch no longer does auto-down, I have to hold the switch down. I've replaced both front "door checks" which are the devices in the hinge area that damp door movement and provide the travel stops. They both failed within 50k miles and have been good to go since replacement. The replacements were an updated part number, so it probably won't affect newer 4runners.
Everything else has been routine maintenance, replacing aftermarket modifications, or problems caused by aftermarket modifications.
17 oil/filter changes, 5 sets of tires, 12 front wiper inserts, 1 front wiper arm replacement, 3 rear wiper inserts, 4 windshields, 1 set of spark plugs, 2 brake pad and rotor replacements, 4 differential fluid changes, 1 transfer case fluid change, 6 air filters, 1 ATF fluid change, 1 coolant change, 2 sets of swaybar bushings, 1 each LBJ boot replaced, 1 power steering fluid change, 3 brake fluid changes.
I just changed the inner/outer tire rods and will probably soon replace the LCAs for new bushings and ball joints. Nothing wrong with my old ones, just piece of mind, really.