Not really sure if this could be considered underrated per se (it got some decent reviews back in the day) but every time I ask anyone if they've heard of it, they say they haven't:
Z
You can't go wrong with beer drinking asshole robots.
ah yes. the duke nukem of RTS..
Anyways, how about Mount&Blade and the Age of Pirates series? Both of them had crappy graphics and some gamebreaking bugs, but I think they had some innovative sandbox type battle systems created for the PC. Mount&Blade had this awesome velocity based combat system and horseback archery. While Age of Pirates had this Caribbean ship battle sandbox going on. But the cool thing about them is that you can start building your own army and declare war against the rest of them and actually win it.
Then there's Red Faction: Guerrilla which utilized destructible structures as an integral part of their gameplay..
There's also the Total War Series and King Arthur which are some of the best strategic games I've played.
Spore and Black&White series had this dynamically organic like system that would've been cooler if they didn't try too damn hard to be "funny" with their juvenile antics and failing so miserably.. Though I would've liked to see a version of those games aimed for more mature audiences..
There's also the Majesty series with their wacky bounty-based RTS system.
Vampire the masquerade, which had a great story and setting, but would've been cooler if it was more sandbox and less railway.
(I wish more games from White Wolf could get their own PC games, especially Mage the ascension.)
There's Impossible Creatures which is an RTS game that allowed you to create the unholy fusion of whatever creature you could imagine. Just think of an army of great white sharks running around with cheetah legs..
And then there's Paranoia..
which tells you to trust the computer 'coz the computer is your friend.
(which is like having the unholy offspring of HK47 and Glados becoming the human overlord)
