for me:
Robin Hood Legend of Sherwood:
The art style and gameplay for this game was amazing. It was also by a budget German company as I'm aware.
Command and Conquer Tiberian Dawn:
This game was utterly astounding. It took all those crappy turn based games (not that theres anything wrong with those) and showed them whos boss. This game in my opinion was done so well in every way that I prefer it over every other command and conquer game (Tiberian Sun being an exception). There just so many great memories here.
Rome: Total War:
This is one of the greatest RTS games I have ever played. I LOVE the Total War series but Rome is my favorite because it took such a leap from Medieval 1 and all other RTS's in the genre.
Blake Stone:
Makes DOOM look like crap in terms of originality and gameplay. GO BUY IT HERE NOW!
... these arent really my top 3 just what i can remember right now :P
what about you?
Although robin hood is my number 1

1. Quest for Glory 1-4: A merger of adventure gaming and RPG! What's not to like?
2. Ultima. Pretty much all of them, although there are several I haven't played (and I've only completed about four).
3. Blade Runner
Mind you, around here these aren't going to be considered unheard of, and possibly not underrated either due to our rather unique community.

1. Rogue Trooper
2. Discworld Noir
3. Panzer Dragoon Saga

First of all, Command and Conquer and Rome: Total War are far from being unheard of or under-rated. They've been pretty much universally enjoyed by all serious gamers who are older than 16.
As for me, I'd have to say:
1. Space Ranger 2
2. Madballs: Babo Invasion
3. Stronghold: Crusader

1. Space Rangers 2
2. Armageddon Empires
3. Kohan series
Honorable mentions to AI War, Depths of Peril, Rogue Trooper, Starshatter, and the Strike Fighters 2 series of games.

Magic & Mayhem
Alter Echo
Gitaroo Man

Hell ya!

Snatcher - Excellent Cyberpunk adventure game released in the US for Sega CD. While it has a cult following in the US, it never really received wide spread success.
Call of Cthulhu - Dark Corners of the Earth - Awesome game based on the Lovecraft Mythos. The only real downside of it is the extremely high difficulty curve early on due to you having to escape the townspeople, but the storyline is great, and holds you till the very end.
Vampire: The Masquerade - Bloodlines - Extremely fun game based on the Pen and Paper game. The fan patches have greatly improved upon the initial game, and has two of the creepiest parts of any game.
RUNNER UP!
Shadowrun for Sega and SNES. We need a real, next gen version RPG/Adventure. Preferably an MMO.

I am playing through The Saboteur right now and I have to say it is an amazing game with a solid PC version (despite no AA) and the fact it is getting no attention what-so-ever is a shame, so maybe that one.
Another example for me would be Timeshift, which I honestly think is one of the best FPS games ever made on PC and it gets no respect at all except from the few who played it.
Risen is a stunning RPG that was quickly forgotten about and ignored due to Piranah Bytes' Gothic 3 travesty, which is a shame. That game is better than Oblivion for my money.
Darkest of Days is no classic but on PC at least it is a solid and interestingly different FPS game that pretty much no one cared about at all.
I feel like lately almost every game without a AAA budget or hip indie status is quickly ignored. It's like the fading middle class, only with games.

1. Hardwar
2. Woodruff & The Schnibble
3. Amber: Journeys Beyond

You Sir, are my new hero!

That game was awesome, I still occasionally play the Sega version on my PS2 (AR Max Sega emulator). It would totally make a great MMO, as long as it had one of those microtransaction based, "real world" economies that allowed you to invest real money in it and possibly make money off it, like Entropia Universe and others.

Rise of nations(not so much underated as underpurchased)
It didn't really bring anything new to the table but it absoluteky perfected the genre, still the only game I play online even today.
Sacrifice(similar to above)
This game is kind of an example of what happens when dev's try to do something a little different, people are unsure if it's their kind of game as a result don't part with the cash. the ingenius thing about this game(at the time) was the way it clipped the distance to improve what you were really looking at(If you buy it now it won't clip because video cards are so much better than what were available at the time). If your looking for a new game I believe this is on GoG, Worthy purchase.
KKND(Krush Kill & Destroy)
KKND was a post-apocolyptic game similar to C&C with great video sequences and well scripted levels, Didn't get anywhere near the sales of C&C, seems pretty rare now too.
None of these are exactly unknown or anything but they didn't make the kind of splash that some of their counterparts have. It's weird how some games are so highly rated now but nobody really noticed them at the time.

Nexus: The Jupiter incident
Barely anyone seems to know this excellent real-time strategy ... star-trek-ish game? :D And that's really a shame, it's unique in it's genre and really worth playing for it's story and spectacular space battles
Call of Cthulhu
Critics loved this game, and yet, not too many people have played it. Still the scariest horror game I know of.
Armageddon Empires
Postapocalyptic turn-based card wargame. What else should I add?
And, I would probably throw Jets'n'Guns in as well. This sidescroller is definitely one of the best games of it's kind I have ever played, it has excellent soundtrack, nice, humorous style and lots of explosions

Being a history major, I was all over the development of Darkest of Days, and couldn't wait to play it. I beat it in 2 days, and it was obviously a low budget title, but it was actually GOOD, with an interesting storyline (for me anyways, other people find history boring) that kept me wanting to play it, and the Pompeii mission alone justifies purchasing it. I did laugh when Dexter said "This is why we can't have nice things" after the enemies kill those civilians however, and then proceeds to hand you the most powerful weapon in the game.
Interesting note: On my history exam this term, I had to write about the strengths and weaknesses of the North and South of the US Civil War, and I actually used the Battle of Antitem as a focus point on the loss of the South, partly inspired by the game, and because the teacher never really covered the civil war in class -_-