Snobs will try and bring up Herzog Zwei, but really, the RTS genre as we know it starts with Westwood's classic Dune II, which, while playing a little rough around the edges these days, still looks amazing.
Being so old, though, many of you might not have played it. Not to worry. Here's a version of the game running in HTML 5, meaning it'll spin along quite nicely right in your browser. You can even play some multiplayer if you're feeling up to it.
Dune II [Dune II, via Prosthetic Knowledge]