The only games where I actually go for 100% of everything are the LEGO games and the Batman: Arkham games.
Interesting that you mention the Arkham games, because I've avoided most of the extra stuff in them. Just never found them appealing. I could never figure out most of the Joker stuff, for instance, and I'd always be distracted by something else and never get back to them. There was just too much other stuff to do.