SpooferJahk: Serious Sam 2 - While it wasn't critically panned, I have heard a lot of hardcore Serious Sam fans hate this game to oblivion because of the cartoony style of the game. Personally, I actually enjoyed the cartoony style of the game because it made what was already a pretty bad acid trip of a game world even more insane. Plus, it's the classic Serious Sam we all know and love, with more to it like vehicles and more varied environments, which is a big plus in my book.
I haven't actually played Serious Sam 2 yet, but having played Serious Sam 1, I always thought that part of the appeal of the Serious Sam games was that they were, well, not particularly serious and quite silly. That's what I liked about them at least, so I find the super over-the-top cartoony style of Sam 2 pretty appealing. I can see why some would complain some of the character designs go a bit far, but I think it suits the series pretty well. I mean, this is a series where you fight headless screaming kamikazes with bombs for hands.
As for games I've played that are disliked, there are a few.
Crash Bandicoot: The Wrath of Cortex on PS2 seems to get a lot of flack as the start of the downfall of the Crash series, but I was personally quite happy with it and it gave me everything I expected from a Crash game. Just a shame about the loading times.
Mischief Makers and Mystical Ninja Starring Goemon, both of N64, got pretty underwhelming critical reception at the time, but now they're often consisted classics by N64 fans, so I'm not sure if they'd qualify. I think both games are superb though.
Also on the N64, I liked the Bomberman games a lot. I haven't played Second Attack since it was never released here, but I felt Bomberman 64 did an excellent job of bringing the classic Bomberman formula into 3D, and Bomberman Hero was a solid platformer that managed to feel like it was doing it's own thing and didn't rely on copying other successful platformers like Banjo Kazooie or Mario 64.
Also, Castlevania: Lament of Innocence. Yeah, it's no Symphony of the Night, and it borrows a bit too heavily from Devil May Cry (some of the animations even look similar), but on it's own I felt it was an enjoyable action game with some excellent music.