Billy Hatcher and the Giant Egg is a game that isn't very well known as far as I can tell, and I adore that game to death and I wish it got more love. It's a game on the GameCube about saving Morning Land from eternal darkness by wearing a "Legendary Chicken Suit" that grants you the ability to roll huge eggs around and defeat enemies with them. The game is a pleasure.
Another game that people do know about but don't really appreciate as much as I do is Super Monkey Ball Banana Blitz. People shrug it off when they see that it's one of the games that use the newer redesign for the characters, and while I do agree that the series did roll downhill around that time, Banana Blitz was new and unique. Motion controls are definitely interesting and I think it's a fun and fresh new way to play Monkey Ball, but the characters have different stats and I love that you can use character choice to experiment and strategize for beating a stage that you're stuck on. It doesn't hold up to how great the original Super Monkey Ball 1 and 2 were, but I think it's a game worth appreciating. The music in Blitz SLAPS too.