I've played various RTS games, here is my take on them. It should be noted that this is in response to "Starcraft vs SupremeCommander vs Dawn of War.".
StarCraft: Brood War
Fantastic game and personally, my favorite video game. It combines all the elements needed to make a successful game. It's still got about 1 million active players who log onto Battle.net each day and is still sold wherever games are sold (even though it was released in 1998, over a decade ago). Multiplayer Use Map Settings is what really separates this gem from the rest of the games out there, Multiplayer Use Map Settings on Battle.net, along with stat tracking, ladder, tournaments, live tech support, channels, automatic patching, a anti-hacking/cheating system, ignore lists, forums, friends lists, etc. make Battle.net the most popular online gaming service ever (statistics show that Battle has 10 times more players than Xbox Live).
Warcraft III: The Frozen Throne
Warcraft III is StarCraft, but 3D (and some hero units can hold items and level up).
Warcraft II: Battle.net Edition
Think of this as a pre-StarCraft form of StarCraft. For both races (including the Elves with the Humans), the Orcs and the Humans (which joined together with the Elves) are pretty much the same. There are however, a few small differences between the two races' units' statistics.
Warhammer 40,000: Dawn of War: Dark Crusade
A fun game, I played it on single player. I tried it on multiplayer, it's sort of a rip off of Battle.net, but then again, so is pretty much everything else since Battle.net was the first online gaming services to have chat rooms, friends lists, etc. However when I logged in, I couldn't play games, some sort of firewall problem, I tried to fix it but, StarCraft is better so I haven't really gotten around to fixing the problem yet.
Star Wars: Force Commander
This game got horrible reviews, but don't let that fool you, it's actually a fun game. The game is (unlike most RTS games) not based around resource gathering. In fact, you don't even gather resources, you capture enemy (and neutral) Command Bunkers and get command points to create units, structures, etc. The multiplayer for the game could use a little work, it relied almost solely on the Internet Gaming Zone, which is now pretty much defunct (the service exists in name only, no games actually work on it, but it is still a technically a corporeal entity). The game is considered by many to be the first 3D RTS game ever.
Star Wars: Galactic Battlegrounds: Clone Campaigns
Take Age of Empires II: Age of Kings and rename the units "Lando Calrissian", "Luke Skywalker", "Princess Leia", "Chewbacca", and "Han Solo" and you have Star Wars: Galactic Battlegrounds.
Dominion: Storm Over Gift 3
This game is alright. It is kind of a rip off of Command & Conquer though. The game is the "sequel" (more like spin-off) to G-NOME, which is a combination of a Mech Simulation, First-Person Shooter, and Third-Person Shooter. However, unlike G-NOME, this is a RTS. So you have the same four major factions (not including Sheridan Rebels, since they all died in G-NOME), these factions are the: Union (Human), Darken, Scorp, and the Bendian Mercenary Provisional Republic (Merc). The game is extremely glitchy and had several problems in development. One such problem was 7th Level (the developer and publisher of G-NOME and Dominion: Storm Over Gift 3) going defunct, as well as the company that picked up the title (Ion Storm not knowing how to make a game, just like the new publisher ( Eidos Interactive) didn't.
Age of Empires
Originally a good game, however, it needs better multiplayer.
Age of Empires II: Age of Kings
Age of Empires but with better graphics.
I've only played the demo of this, but it seemed like it had potential. It has a few problems though, there is absolutely no way of knowing what to do in the game (as there are no instructions), and nobody plays it. It has a system similar to Battle.net, however, unlike Battle.net, nobody is ever on Strifeshadow.
Star Trek: Armada
A fun game with a system similar to Battle.net (that system is called the World Opponent Network).
Star Trek: Armada II
Not as good as the first one.
Star Trek: New Worlds
Not worth buying, it doesn't even work (not right anyway) on Windows XP.
Supreme Failure (I mean Commander)
Chris Taylor forgot how to make a RTS and so he made a game that was worse than Cybernoid (don't download that game, if you do, you might kill yourself, but you have a better chance of killing yourself if you go on the official Supreme Commander forums). Unfortunately two forums modeled themselves after the official Supreme Commander forums, these forums are The Warcraft Occult (The Warcraft Occult isn't quite as bad however), Forum Sector (don't click the link to Forum Sector, it is a child pornography site [it used to be a StarCraft fansite, but then rustyslacker joined and started posting some stuff, including bad pictures]).
Extremely awesome, it's just like Battle.net, you can play for free on PhoeniX WorX.
Total Annihilation: Kingdoms
Not as fun as the first one, but still fun, nonetheless.
Don't buy this.
It's pretty fun, and different.
Command & Conquer: Red Alert
Command & Conquer: Sole Survivor
Command & Conquer: Red Alert II: Yuri's Revenge
Command & Conquer: Tiberian Sun: Firestorm
Thank god I'm done with the Command & Conquer games, now then, Battalion Wars. Battalion Wars is a console RTS game (for the Nintendo GameCube). It is fun.
A Dune game! But Frank Herbert's Dune Online is better.
Age of Sail
It is very slow paced.
A fun MMORTS game.
Warcraft: Orcs & Humans
Where is the Battle.net?
Theatre of War
One of the oldest RTS games that is still on the market. This came out in like 1994 and you can still buy it.
Shogun: Total War
I haven't really had much experience with this game, so I can't say much about it.