Despite their weaknesses, I liked both of these games. I'm tempted to play 12 again when the remake comes out. I know next to nothing about 13 and 15, but I may try the latter at some point if I can convince myself that I have the patience for a JRPG anymore.
Super Bust a Move
This is my favorite version of Puzzle Bobble, between the music and that one creature that vomits on the title screen. (I always chose him.)
Klonoa 2
Though clearly inferior to its predecessor, this game was worth playing as well.
Ratchet and Clank 1, 2, and 3
I avoided all of the PS2's comedy mascot-oriented 3D plaftormers for years. It was only after playing Beyond Good and Evil and wanting more that I decided to try this series, hoping that it would have at least a fraction of the appeal. I found the action, upgrades, and colorful worlds compelling enough to make up for the irksome story and characters. The second game was my favorite of the three, and I played it through again on PS3 not long ago.
Beyond Good and Evil
I technically played this on GameCube, but I assume the two versions are nearly identical and it's hard to resist mentioning it. This was a game I bought used and somewhat blindly, and I was surprised at just how good it was. I played it again a few years ago on PS3 and it still held up. Maybe one day we'll see that sequel.
Silent Hill Origins
I already mentioned the other PS2 Silent Hill games, as have other people, but this is one that was probably overlooked more than it deserved. It was by the same team that made Shattered Memories, but more of a traditional Silent Hill game. Though I would rank this title below the others, it's still one I'd recommend.
Sub Rebellion
It's already been mentioned, but this was another game that really impressed me. I liked how tense it got when you went too deep and heard the creaking metal. Like pretty much every Irem game, this one had a lot of character.