I'm actually pretty nice to my games, although I've known that I've mysteriously lost some... I find them months later, though, like Pokemon Sapphire. lol
Actually, I think the only ways I've screwed up my games is internally:
My Pokemon Gold's internal battery has run out (no big surprise there, perfectly aware that it's normal)
One of my OoT carts has funny feeling controls, not sure how to describe it... messing with a Gameshark too much or something.
Pokemon FireRed's been screwed over by hacking the crap out of it

I could restart and it'd be normal, but I don't really care that much
I think I messed up my Mother 2 (on M1+2) file a bit by doing the exit mouse glitch, now the game thinks I'm in the prayer cutscenes while walking around. Again, I could start a new file and it'd be fine.
I get the feeling I've messed with another game, though...