Bandits: Phoenix Rising. I know I can think of more, I'll edit them in later.

Totally agree. Basically Civilization in real time.
Funnily enough, I played the demo to death. Bought the gold edition and have hardly touched it.
I also second Call of Cthulhu.
Might throw in Full Spectrum Warrior and Silent Storm.
Full Spectrum Warrior because it was "different". Wouldn't be surprised if it inspired Brother's In Arms. You've got a small, modern squad in a fictional Middle Eastern country where someguy has done somebadthing and the US goes in to clean up the mess.
It's all real time, looks rather nice, and plays well. You take the part of an invisible commander, set fire radius', flank, deploy tubes, smoke and so on.
By our dearly departed Pandemic. *sniff*
Silent Storm was also pretty cool.. It didn't get much shelf time here in Australia. Turn based WW2 (albiet fictional) combat, destructible environments, character levelling and customisation... Heeeeey... Speaking of, it WAS distributed by JoWood... How about it, GOG?

Drakkhen - And awesome old 3D RPG! if you hear the wind blowing ... RUN!
Thargan - Was one of Silmarils adventures (like Starblade, Maya, Colorado, ...) and was one of the first in wich you can control a BIG Barbarian sprite in a PC Game (Do you remember those ridiculous small figthers of Barbarian ...)
Starblade - Another Silmarils adventure (The first PC Game in wich you have a LIGHTSABER!) One of my personal favourites!

Rise of Nations was pretty well loved among RTS fans I thought. Rise of Legends would be the underrated one, if it not actually terrible. Obviously I never played it.
I agree with Cthulu as well.
On to adventure games there is an oldie but goodie called Blue Force that is like Police Quest only actually good. It is way too short and has no voice acting, whcih I find hard to deal with now for adventure games for some reason, but I remember it being good.
Another adventure game would be Rise of the Dragon which is part of the often overlooked cyberpunk genre and has a real edgy and mature vibe.
Both those adventure games I listed are abandonware and free for everyone.

I know a lot of hardcore FPS fans who liked Jericho as well, though I myself never played it.

Fenixp actually liked Jericho too. Come on, you can play an asian chick with katana and a pistool. She's like banshee from WH40k

Penumbra, the first one.
The other two wasn't worth playing but the first one I really enjoyed.
If anyone wants to try out something more unique try it out.

In no particular order.
-Pathologic
-The Void / Tension
-The Path

I'm actually playing this right now.

As a warning, this post contains minute biased opinions and might not be a good read for everyone. Hopefully I feel like writing about the two other games I feel are too underrated, but you'll have to excuse me if I take a short break.
1. System Shock (1994)
While being regarded as one of the best FPS RPG hybrid series for the PC, the System Shock series, whenever asked about people only ever mention System Shock 2 being their favourite game. These people praise the storyline, setting and diversity in gameplay, but fail to see that all of these aforementioned elements are more intricate and presented in a more colourful and thoughtful way in its predecessor.
This is not an uncommon occurrence, either. It's everywhere; online forums, YouTube video comments, instant messengers and IRC. You can try it yourself; bring up the System Shock series and see the discussion "evolve" into exchange of people's memories of System Shock 2. This is further demonstrated by the massive difference of 2 567 (at the time of writing) wishlist votes here on GOG.com -- wouldn't you think that a fan of even just one game of the series show and give their support for all the games in order to allow more and more people to eventually enjoy them?
System Shock 2 marked the change of the company with Irrational Games taking up a lot of the work with the game which shows in the final product. While all the Thief games (yes, even Deadly Shadows) for example are consistent in storyline and atmosphere together. System Shock 2 on the other hand, feels like an attempt to incorporate the characters and basic ideas of System Shock into an eccentric first person shooter, instead of trying to create a true sequel to the original game.
I also feel that Shodan didn't have any reason to be in System Shock 2, Xerxes was a completely interesting concept and would have been great if they only went and explored further with it. I know Shodan is the flagship of the series, but since they decided to went with a so different concept altogether, some minor references to Shodan would have been more than enough. Now it feels forced and makes the game stand out as Looking Glass Studios' last cry before they faded out of extinction with Irrational Games picking up the pieces.
I can't and won't deny that System Shock 2 is a fantastic game, which it is, I just don't feel like it aimed at all for what it could have been. It's kept me confused for years, trying to figure out what were they going for. While a lot of the new functionality, such as the inventory system and the replicators were a welcome addition, a lot of the newly added things feel distant from the dark and oppressive atmosphere present in the first game.
To demonstrate this further, whereas in System Shock you can see the station's story evolve around you as you go about it. Damaged systems you must bring back online, bodies surrounded by the remains of gunfights and environment turned to rubble by the acts of cyborg armies controlled by Shodan. System Shock 2 presents Von Braun in a very clinical and orderly fashion where the most history of struggling you see is a trashed table or an explosion decal on the floor.
The whole horror aspect of cyberpunk is well implemented and maintained in System Shock with the use of music and sound, lighting of the levels and unorthodox level architecture that make you step carefully into each room. System Shock 2, in my opinion, solely relies on few terrifying monsters and maybe one or two areas built to enhance the fear of solitude. They did have the ghosts and some personal logs that seemed very interesting in the horror aspect, but it seems they completely forgot about those when you proceeded on to different decks. Forgetting to use the resources they had so prominently started working on seemed to be a common problem with the game.
One thing I highly regard in the first game is in how many ways it revolutionized the FPS genre which was already becoming stale from all the Doom clones (I personally love Doom but I doubt anyone wanted to play each and every one of those endless second rate clones). To my knowledge, System Shock was the one of the first FPS games to incorporate such things as leaning, crouching and proning to the player controls, free on-screen mouse aiming (which was also in the Raven Software's game CyClones, the same year), multiple firing modes and ammunition types for most weapons, throwable grenades and projectiles with proper physics and even jumping in low gravity that had not been done before. Not to mention destructible environment not limited to just one or two objects.
What did System Shock revolutionize within the FPS genre? I can't come up with a single thing so suddenly. I'm sure there's one or two minor things but most of the "new things" it created we're either borrowed or a semi-clever combination of two things that had already been around.
Another thing that completely baffles me is the main character and he's introduction in the game. After the intro -- which is pretty much a showcase of Shodan quotes from the first game and some silly Paul Verhoeven style news footage to introduce the player to the ships. Then they jump to a silly "character creation screen" similar to the one in Morrowind, which, in my opinion, completely kills the pace. After that improper Macarena dance, when you finally end up on the ship, you're given the most stupid way to evade any proper scenario explanation: You're devoid of your recent memory, albeit just completing a three year character creation and a training mission. It seems like they ran out of storyline writers after they cooked up the Shodan parts and just scrambled a random mess together.
The first game handles this so much better, after the intro you take the logical step and enter the aforementioned cryogenic healing coma. Logically, you wake up after the automated process and are introduced to the wartorn space station without any kind of pauses or amnesia silliness. I wish the second game had put you right into the action, but allowing you to "remember" your character specialties in certain key areas.
Irrational Games seemed to completely disregard the original hands-on feel of the original; where in System Shock the augmentations had a visible function that helped you personally to solve the game -- System Shock 2 just gave you completely ethereal character stat boosts that never notably affected the game in the end.
Puzzles in System Shock were as well very hands on; there was always an electric circuit you had to manually reroute or similar panel to fix. System Shock 2 left you with a MineSweeper clone or with the simple task of finding the proper keypad code. In the first game, having to manually reload the weapons and change their firing modes only intensified the feeling of the hacker's job, though, the change from these to the press of a key on your keyboard were a welcome and a logical change.
Still, I feel like a lot of System Shock 2 had been consolized. Maybe they rushed the game or maybe that was their point all along -- whatever the case, I don't follow their reasoning and am left quite cold with the final product when in comparison with the first game.
It's a sad I have to specially wish or even compel for fans of System Shock 2 to try out the first game, they don't seem at all interested seeing how positively different it is. I want to see System Shock 2 on GOG as much as you do, but if we get lucky enough to have both games, I'm hoping at least more than one of you SShock 2 fans will grab and try the first game out.
Here's the intros to both games for good measure:
System Shock intro
System Shock 2 intro

Uplink. : It was a single unchanging screen but it was FUN. You had to hack through various computers to achieve your goals, there was a storyline that would, and often did, progress forward with or without your help, and it had a randomly generated placement of the various servers that you would hack for fame and profit
Echoing Daedolon's post, I too find System Shock 1 to be a superior game to its sequel because of the hands on feeling, a much more coherent level design and a tighter story arc than its successor. I do have to correct Daedolon in that Ultima Underworld 1 and 2 had all of System Shock 1's innovations before hand, they just weren't as widely recognized, in my humble opinion, until System Shock.
Also SPACE RANGERS 2 !!!!! Digital Crack in game form consisting of the "just one more turn and I swear to all that is unholy that I will go to sleep....wait, is that SUNLIGHT coming through my window?" syndrome.

Heres mine
Eternal Darkness (gamecube)
Valkyria Chronicles (PS3)
Zack & Wiki (Wii)

I agree with you that first System Shock is superior to System Shock 2 - note that I have played SS2 BEFORE playing SS1. And yes, you are right that almost EVERYONE played SS1, but no one seems to care about SS1.
To sum it up, things I DO actually love about SS1:
- Audiologs. No game after SS had such a great audiologs - seriously, they were awesome, VERY well written, and voice acting was worth it too.
- Difficulty settings. Seriously... This game got it right. One could set it to fit his needs.
- Puzzles. Yes, those connecting puzzles were AWESOME.
- Freedom and secrets: This game really encouraged exploration. There was tons of stuff to be found, and every time I play this game I find something new. And one REALLY had a feeling he's on a space station - design of various levels was great and believable, and you got real freedom of movement on it, so it actually felt like you were walking trough CORRIDORS, not THE corridor...
- Details. Your body actually smashes itself to the wall it you hit it fast - when you have speed booster, you'll get hurt. Your heart beat speeds up according to your exhaustion. Drugs have negative effects. And there's much, much more...
But, as far as implants go, I actually found SS2's RPG system more interesting, and I LOVED SHODAN in SS2.

Don't forget the cyberspace segments in SS1! I actually liked those....

All? :)
Well I have to agree on that most of the stuff were there, still with System Shock I feel they upped the stuff to a new level and added yet quite a bunch of new, appropriate innovations. System Shock 2 just seemed to draw from other games of the same time without really going for anything new. I also acknowledge that the Ultima Underworld is another way too underrated series. It seems to me that Looking Glass were the masters of atmosphere and innovation back in the day.
I also loved Uplink, if only it wasn't so unstable...