This is super difficult for me to even decide upon, let alone answer. I have a ton of games that are my favorites. And I mean they would probably weigh a metric ton. But, I think I can narrow down to two in particular that I seem to endlessly replay.
E.V.O. The Search for Eden
I just love this game. Absolutely love it. The first evolution game I ever had been aware of. I loved the design, gameplay (as monotonous as the grind could be), the vast array of ways to evolve, the secret evolution paths and crystals, the small semblance of a story, and the progression throughout the ages. Considering I have a passion for science, my interest and enjoyment was only multiplied. This is a game I would love to see Square Enix (Enix side) revisit.
Final Fantasy Tactics
Just one of the best story lines in any game, ever. I am completely enthralled by it. I actually enjoy the strategic combat, sprite and world design, the many jobs, and insane amount of replayability. I always play this game to completion at least twice a year. And it never gets old.