What exactly do you mean by "wrongly ignored"? As in ignored by the press, tossed to the bottom of the barrel by consumers, or blatently put off by developers who only realized later on that they had a hit on their hands, but let it fall on its ass and never get up until it was too late?
Anyhow, just for kicks, let me toss a few wrenches in here for y'all. I've played all of these, by the way, and am not just suggesting them:
Parasite Eve 1 & 2
The Magic School Bus in Outer Space (yes, I loved this game when I was younger...)
Oddworld: Stranger's Wrath
Bloodrayne series (the games that inspired Uwe Boll to fuck it up)
Breath of Fire III (remade in Japan only... and i have it on my PSP XD)
The Bard's Tale
(dot)hack *the first series*
Seiken Densetsu 3 (Secret of Mana 3... never released outside of Japan, but they should >.<)
Bugs Bunny's Crazy Castle
Fatal Frame/Fatal Frame 2 (some of the best pants-wetting horror that you can get, except its kinda hard to find anymore. although there's a fanbase, not enough people appreciate these games)
And many more of which I can't quite remember right now... A few of these got fairly good, even excellent, review scores across the board, but were completely ignored by the masses because they didn't have "Square-Enix" or "Bungie" tacked onto their respective boxes, or they just didn't make due with the publishers who saw low sales as bad figures. I'm still waiting on a sequel for The Bard's Tale, and probably will be for a long time, if it ever comes around...
And I'm pretty sure if I say "Persona", there'll be like one other person who'll respond to that saying "Hey, I remember that!"... I have the original (w/ case but no manual >. *long story*
BTW I wouldn't consider most of the games posted in here "wrongly ignored". For example, System Shock 2 has a HUGE fanbase following, Grim Fandango was only ignored by LucasArts, and many others follow likewise. And yes, I own a Sega Saturn ^-^. It sits next to my Dreamcast, but needs a little more game love >.> Ebay is the only place to find them anymore, and that's so freaking expensive more often than not...