Ooh... this is a hard question. I've played a lot of games over the years on many different consoles and handhelds, and there's quite a few I hold near and dear to my heart as favorites, so it's difficult for me to pin down one in particular as my all-time favorite game. After thinking about it, though, I guess I'd have to go with my favorite Playstation 2 game, Ratchet & Clank: Up Your Arsenal, as my all-time favorite. The game really had a sense of polish and finish that showed Insomniac Games' care over game design and attention to detail.
There's quite a lot I love about it: the story was entertaining, the gameplay elements were really refined and improved over the second game's, the multitude of weapons and their upgrades were fun to use in different ways, the soundtrack by David Bergeaud was phenomenal, and the voice-acting in particular was top-notch. You can tell James Arnold Taylor had really grown into his role as Ratchet by this point, and compared to his performance in the second game, as well as other games he had done VA work for, Final Fantasy X in particular, you can see he put a lot of passion and heart into the little wrench-slinging Lombax. David Kaye really got to stretch his legs with Clank, and Armin Shimerman was hilarious as Dr. Nefarious.
All in all, I highly rate R&C:UYA as my favorite overall game, because it's the one I ended up sinking so much time into and really appreciated the whole package it provided.