I just pulled the rear wheel off the bike for the first time yesterday. One of the POs had the brake rod running up over the swingarm, and the lever it connects to was pointing skyward. The paint had rubbed off where it was touching of course. In my quest to set things right on the bike I put everything back to the way it should be. It was a pain to get the lever off, and a pain to get it back on. The bolt that clamps the lever to the brake assembly was chewed to hell and wouldn't thread back in at all. I ran a tap through the lever and replaced the hex head bolt and solved the problem.
Not to mention the "roundish" lock nuts on the chain tensioner bolts. I mean, If you don't have the proper wrench, just leave the f*@&*ng thing alone! Unless you're stuck on the side of the road of course.
There have been many other things as well, mostly fastener related. I guess I'm lucky in some ways, stripped fasters are relatively easy to deal with for the most part, at least nothing on my bike has had saws, torches, welders, nails, etc applied to it. At least not that I know of.........
Rant over, Lenny.