Kohan was the bomb!
But indeed, cult following may not imply decent market saturation, as Pidesco implies. Perhaps you'll have to do some research to determine what qualifies and what doesn't. I'd certainly say Giants qualifies, but at the same time I hear a fair bit about it in gaming circles. Perhaps Torment, System Shock 2, Deus Ex, Bloodlines? It's hard to tell what's a cult following and what's a common game on a forum like Obsidian.
Psychonauts
Giants - definitely
Beyond Good & Evil
Jagged Alliance 2 - definitely
Anachronox - definitely
Arcanum
Bloodlines
Fallout 1 and 2
Torment - most likely
Total Annihilation - most likely
System Shock 2 - most likely
Deus Ex 1
NOLF - definitely
Thief games
Blood - would be an interesting choice
Spellforce
Undying - definitely
It depends on the target audience really. Arcanum, Bloodlines, Torment and Fallout probably wouldn't be underappreciated by the RPG crowd for example. But Deus Ex 1, NOLF1, Thief, and System Shock 2 may well be underappreciated by the FPS crowd (how many played DX2 and assumed they didn't need to play DX1 because it would be worse?)
Also consider not how well the game was received, or its cult following, but whether it was overshadowed by a big seller (e.g. Half-Life, Quake, whatever) at time of release. Not many people go BACK in time to find good games unless explicitly instructed to. Again, depends on the target audience.