Keep in mind, this isn't really an underrated game thread. It's about games that should have gotten credit for something they were supposed to, but never got that credit for whatever reason.
One of the games I can think of:
Perfect Dark (N64)
Though a very popular game (not as much as it's predecessor, Goldeneye 007), it still doesn't seem to get the credit for being the first game published by Nintendo (this was back when Rare was still with them) to bear the ESRB rating of M for Mature. Instead, the FAR less popular, Eternal Darkness: Sanity's Requiem (bear in mind, I'm not trying to slam that game as I haven't played it yet, though I can say in terms of gameplay it looks like a fun game, but visually, I've seen a lot better in the era the game was released in) takes most, if not all that credit. This always confuses me whenever someone like ScrewAttack's Stuttering Craig or former CGRUndertow reviewer Jen mention the latter as such when I recall Nintendo publishing games for that audience sometime before.
Not to mention, I believe there was a newscast where they made a big deal out of Nintendo and their involvement with Perfect Dark, saying they have changed from making Mario games.
What games have you found that doesn't get the credit it deserves?