The Legend of Kyrandia series are a wonderful but unknown point and click adventure.
Loom is pretty great. There's no real replay value, but I've played through it a few times in the same way I'd watch a good movie over again.
Planet's Edge: Point of No Return is an incredibly unknown game that's absolutely epic and amazing, though it'll be quite dated today.
Dunno if the Quest For Glory series is considered obscure. I'm pretty sure it is. And they're probably my favourite series of all time.
X-Com is a game that non-gamers wouldn't know, but every single gamer knows it and of its legendary status, so I guess it won't count.
Star Control II - same as above.
Syndicate was also really awesome for its time, would be a bit dated today, but was amazing back then.
Crusader: No Remorse, I'm pretty sure isn't very well known.
The Ultima series is a household name, but I don't think very many people have actually played it. But most who have tend to list Ultima 7 as among their favourite games ever, and imo for good reason.
If you like old school and you like wrestling, and you want a really good game that's more like a wrestling simulator rather than how Smackdown vs Raw is simply a WWE simulator, then Fire Pro Wrestling is probably the game that has sucked the most time out of my life than any other.
Hexen was a fun little game. Basically a Doom rip-off, but more medieval.
Darksun: Shattered Lands, and Wake of the Ravager are spiritual prequels to the Forgotten Realms games, and will feel really dated now, but for my money are some of the best RPGs I've ever played, considering its time.
The Incredible Machine is fun for a little bit, just to include a good little casual game on the list. Gets old kinda quick, though.
American McGee's Alice - dunno where this stands. Casual gamers won't know it. Lots of gamers know of it. Not the best actual game, but it's worth playing just to experience the art design and re-interpretation of Alice's Wonderland, but this time the dream world has been ravaged by Alice's dementia.
Is that good for now?