Vagrant Story - A game that really stands out for me is this classic title. Its New Game+ feature makes it easy to replay again and again though, especially for that Grand Master Breaker score/Riskbreaker Rank for boss fights that takes a VERY long time to get to, making each New Game+ worth every minute. Not to mention all the weapon and armor drops from enemies there is to get.
Yu-Gi-Oh! Forbidden Memories - is another one that I always replay. I've been meaning to write down what combinations work and what doesn't when combining/fusing cards too, but there's already a guide that covers it, so I might defer to that.
Front Mission 3 - With my memory being so bad, the very long story of Emma's storyline I forget a lot about shortly after playing it, so I end up replaying her story a lot.

Chaos Legion - one of my all-time favorite PS2 games that I'll play again and again and again, even after crushing the final boss with Thanatos' Perfect Form. Interesting trivia, Thanatos means death in Greek and was the Greek personification of death, not to be confused with Charon, the ferryman that carried the dead souls across the river Styx. A fun game that's hard to stop playing.

Yu-Gi-Oh! Nightmare Troubadour - being one of the few Yugioh games for handheld that uses the Egyptian God Cards, it's one of my favorite.
Dragon Ball Z: Legendary Super Warriors - One of the best GBC games of all time in my opinion, each time I beat it and collect all the characters and cards I start a new game just because it's such a fun game.

Dragon Ball Z Collectible Card Game - This GBA game I play a lot too, after unlocking all characters I start a new game to do it all over again.

I don't think there's PS3 or PS4 games I really replay that much. Although I've had the itch to play Budokai HD Collection on PS3 again.
How about you all, do you have any games you play over and over?
