Boy is THIS kinda my schtick. But to name a few examples -
-Area 51: Blacksite isn't as bad as most people make it out to be...coming across as a CoD Clone at worst. The game was also subject to HEAVY amounts of executive meddling from Midway, so the version we got is the usual butchered mess we normally get when something leaves Development Hell.
-WarFront: Turning Point. It's very cookie cutter, but functional. The only thing that undermines it is the horrendous number of bugs (including not being able to read it's own disk!). While there are no patches for it, there are workarounds should you wish to find them. And it's not every WWII Game that has Exoskeleton toting Nazi's and Godzilla sized Russian Tanks (yes I know they've both been done before, but Weird WWII is always more fun to play than regular WWII). Personally, I'd recommend it to anyone who played Command & Conquer:Red Alert 3 and was severely disappointed with that for it to become a point of RAGE.
-Perimeter, and ONLY Perimeter (both Emperor's Testament and Perimeter 2 can go die in a fire). I never hear anyone bring this game up, and when it does it's always negative. Having sat down and played all three of them, I admit the games can be a bit clunky...at first. When you get around to it, it's not half bad and combines some rather unique concepts with an interesting backstory (which also appears to be the schtick of 1C Company - great ideas and concepts, poor/heavy handed execution. As an example, go play Earth 2160 and you'll see what I mean).
-Abomination: The Nemesis Project. This one just plain astounds me, as it holds three key points in VG History -
1) It was the first of the "X-COM Clones" created (the game was released approx. 1999/2000, a good four years or so before the UFO Trilogy. I currently do not have knowledge of anything released between this and the first major X-COM clone (the UFO Trilogy), and as far as I understand Laser Squad predated X-COM by a few years).
2) A lot of innovations made (such as the Player moving and acting in real time as opposed to the turn based battles of X-COM) were soon ditched.
3) This is possibly the closest thing your going to get to a VG Adaptation of "The Colour Out Of Space" by HP Lovecraft (to my knowledge, and before anyone brings it up - yes I played Amnesia, but that reminds me more of stories like Rats in the Walls among some of the other more conventional tales).
And yet, it remains forgotten. Nobody brings it up in conversation at all, nor is there much Video of it on YouTube (as opposed to some of the others on this list).
-Rise of Nations: Rise of Legends. Again, very cookie cutter, but also rather fun (a la Turning Point). I honestly don't see people bring this one up at all for whatever reason. This would be my top underrated game, if not for...
-Homeworld Cataclysm. Just...Homeworld Cataclysm. The first Homeworld had a great story, but was marred by a few clunky gameplay mechanics (e.g: The Movement Disk. Dear god the Movement Disk). Cataclysm went back and refined on them, and (arguably) took the story telling up to eleven with one of the scariest (and unique) bad guys I've ever seen in a video game before or since. They also fixed that damned Disk and a few other control related problems.
Then along came Homeworld 2, which retconned Cataclysm out of existence...and ditched half the improvements made...