Depends what you like, mate. Heaps of good RTS out there, all with their own quirks and traits.
For sheer polish, go Warcraft III [http://www.blizzard.com/us/war3/] and Frozen Throne [http://www.blizzard.com/us/war3x/].
For sheer fun, I'd go with Red Alert 3 [http://www.commandandconquer.com/portal/site/cnc/cncra3/].
For awesome basebuilding, you're with Total Annihilation [http://en.wikipedia.org/wiki/Total_Annihilation] and/or Supreme Commander [http://www.supremecommander.com/].
For beautiful spaceship action, it's Homeworld 2 [http://homeworld2.sierra.com/homeworld2.jsp].
For spaceships with more complex base management, you play Hegemonia [http://www.dreamcatchergames.com/hegemonia/], or Sins of a Solar Empire [http://www.sinsofasolarempire.com/].
For glorious, violent melees, you play Dawn of War [http://www.dawnofwargame.com/au/home/index].
For quick, tactical, yet complex play, it's Dawn of War II [http://www.dawnofwar2.com/us/home] and/or Company of Heroes [http://original.companyofheroesgame.com/].
For a more abstract singleplayer experience, try Darwinia [http://www.introversion.co.uk/darwinia/] or Dyson [http://www.dyson-game.com/].
For more info on any of the above, hit up YouTube [http://youtube.com.au], Metacritic [http://www.metacritic.com], or Gametrailers [http://www.gametrailers.com].
There are more I've not played, surely with their own appeals, but since I've not, I can't discuss them.
With that in mind, I've played all the ones I've just mentioned, and would recommend them all. Just keep in mind we're talking REAL-TIME Strategy, so I don't want to hear anyone mention Galactic Civilisations in reference to my "more detailed spaceships game" comment.
Though, Anyone should feel free to call me out on those, if they disagree. Discussion is good, guys.
Edit: Oh, and of those, Dyson is free from the linked webpage. Darwinia, Company of Heroes, Dawn of War 1 & 2, and Red Alert 3 are all available on Steam [http://www.steampowered.com]. Sins of a Solar Empire and Supreme Commander are available on Impulse [http://www.impulsedriven.com/]. If you're buying, try to buy from there. Support the developers.