IMO, hidden gem just has to mean it's an obscure game that you really like. For me, there's countless because I like games more often than not when they pique my interests. One man's gem, is another man's turd. Can't say for sure that it's for everybody.
Congo's Caper is a really fun and well made platformer on the SNES, a system already chock-full of good platformers. IMO, more balanced and fun than SMW.
Iggy's Reckin' Balls on the N64, it combines platforming with racing. Not many people remember that one.
Not too many know the Saturn for High Velocity Mountain Racing Challenge, but I feel it's a worthy contender against the OG Ridge Racer.
Alias the game, on the OG Xbox. A decent stealth-action for fans of Splinter Cell.
It all comes back to a matter of opinion, though. I don't think that just because a game sold wildly, makes it the best. Or that it sold poorly, makes it suck. I also think it's probably true that a lot of good unknown games are hidden inside licensed titles that most serious gamers write off immediately, and never even try. Kim Possible on the PS2 isn't just an isolated instance.