I've got a few ideas:
Disgaea DS, if you like turn-based strategy games, currently at about 110 hours and I've gotten only two endings. Also, the Prinny commentary option is pretty great. And who doesn't like having characters deal more than 100k damage in a hit?
Etrian Odyssey 1-3 if you like difficult RPGs, since each takes quite a while to complete, and the third takes at least two playthroughs to truly complete.
999 is also great, been mentioned, I personally couldn't really stop playing until I finished, which meant it took me only a short while to get all endings, but then again, I read quite quickly.
SMT: Strange Journey is quite long too.
If you like Card Based Strategy, Yu-gi-oh! World Championship 2011 is really good, and has immense amounts of opponents to duel.
Chrono Trigger is great and has quite a few endings and provides some replay value.