I've mentioned this one in other, similar threads, but
Perimeter was the first "That looks weird, never heard of it, let's give it a shot" purchase I made on GOG, and it turned out to be great. Definitely the most unusual RTS I've ever played - it almost plays more like a puzzle game than your typical "overwhelm the enemy through sheer force of numbers" strategy title. Be warned, though: there's a steep learning curve, and the game does a piss-poor job of explaining what it expects you to do, so some patience and a willingness to experiment is required.
And of course, I'll give another shout out to
Chaos Overlords, an indie title from long before "indie" was a thing, and the most surprisingly addictive game I have ever played.