I found this game when I was looking for RTSes with tons of units, and indeed, AI War: Fleet Command is an indie game I've played with about 30,000 active units somewhere in my universe. (I forget if I found it through google, or if I found it through someone on these forums.)
The premise of the game is that most of humanity was destroyed in a massive war against very intelligent AIs. And trust me, the AIs are intelligent, and have out-strategied me many times.
here's a trailer for it:
There have been three expansion packs, and the best part is you can get all the expansions and the original on steam for $4.50
the deal lasts for about 23 hrs as of now. If anyone gets this game and wants to play it, contact me at my steam account neurofuzzy. Although... a "round" of this game lasts a very very long time. A "round" is more like what you would play in a week (it's taking over the universe). Because of that, it's not easy to get multiplayer games finished.
On an off-note, they also released a bunch of their sprites for free use among the game-making community:
http://forum.thegamecreators.com/?m=forum_view&t=160865

Why does blue text appear every time you are near?