I don't really think most of the games listed in this thread really fall into the "cult classic" category. I could be wrong but I always thought a cult classic was more of something that was over looked by the majority and somehow found a small yet strong following. Not exactly an under rated game, more so one that doesn't quite become near as popular as the more prominent titles. And the fact that you, or the majority might not like them, or have even thought of them, is kind of part of the idea, that's why in the first placed they were over looked or became obscure in the first place, not everyone is supposed to like them, I think that's how it's supposed to go.
Some games that I think may fall into the cult classic title, even if a few are relatively new,
God Hand
Alpha Protocol
Deadly Premonition ?
the Longest Journey
The Binding of Isaac
System Shock 2 ?
Resident Evil before 4
Resident Evil after 5
Syberia and Syberia 2
Zork ?
Fatal Frame ?
Valkyria Chronicles ?
Those with question marks are ones I'm not sure of, but I think they count. I think each of those has a following, has a strong group of fans that care for them, but each title doesn't meet well with public eye too often. Resident Evil, I think funny enough is one of the best examples, back during Resident Evil CODE: Veronica there were small groups of die hard fans spread over the internet. Each installment I don't think was ever all that popular with the gen pop and critics. The REmake came along, got some nice press here and there for it's lovely visuals, but then 4 really take the cake, and the series was no longer some fainted heard of thing, it was a house hold gamer name, come 5, come disappointment and people are, I think, helping it go back into the obscure category, less and less seem to be playing it, or caring about each new title, the only thing that really has kept it alive in the public eye has been the love for 4 and the amount of awareness of the brand now. But who, really wanted to touch 6 or Operation Raccoon City, and I think it's that general idea that leads a game into cult classic territory.