Sooooo... I've never actually played an RTS before, I typically play more TBS. I'm sitting on some supposedly good ones (Defcon, Men of War, AI War). So what would be a good RTS for a beginner in the genre?

Age of Empires-it's how I started.

I'd recommend WarCraft 2 or StarCraft 1 if you can get a hold of either of them, although Age of Empires is also a very good suggestion.

Warcraft 1&2 or first C&C games.

If you're extremely cheap, you could give Warzone2100 a go.

So I'll probably get the C&C collection while it's on sale for only $9 on amazon (shame it's an origin exclusive though). Some of you were saying to get Warcraft 1 and 2, but those are kind of hard to get a hold of, and I though that the general concensus was that Warcraft 3 was the best one?
Edit: Also should I get Age of Empires 2 HD or 3 (those are the ones on steam) or should I try and track down a copy of the original?

Not at all. On a lot of these, actually ;)

Warcraft 1 can feel quite dated, but 2 is still an excellent game. Three is a somewhat different beast, with a higher emphasis on unit control and RPG-like leveling and equipping of heroes. It's a good game, very good, but most fans of the series still consider Warcraft 2 to be the better game. All the same, both are very much worth playing.

Age of Empires... again, 3 is a fairly different beast from 1 and 2. Both of those were excellent games for their time, and even today. Almost everyone considers AoE 2 to be the best of the series, and AoE 2 HD is a decent effort, though I feel it's overpriced. You can still find the Gold edition of Age of Kings in bargain bins out there, and with the fan-patch and recently-released fan expansion, it is arguably better than the HD release. There's some work being done to release the fan expansion as DLC, but when and how expensive is unclear. Verdict? Wait for a sale, at least. 20 just seems too steep.

Also, the first three CnC games are freeware. There are patched-up versions somewhere out there, and chances are they work better than whatever EA is offering. Absolute classics and well-worth trying out.

As to the best in the genre... probably Total Annihilation and StarCraft. I'm not really sure if they're beginner-adequate, but they are probably great enough classics that one needs to try them at some point.

Out of those I'd go for Men of War first.

Yeah, I don't think I ever played the first one, but I definitely prefer 2 over 3.

Edit: Actually, it's funny. When I think about it, there are a lot of game series where my favourite installment is the second one. Warcraft, Settlers, Civilization, Heroes of Might and Magic... I know there are more, but I can't remember which ones right now.

My first RTS was command & conquer 1. I played Red Alert 1 too. I stopped enjoying RTS after those. Too complex I guess.

My first RTS was Dune 2 (why no Dune 2 GOG?) still have fond memories of trying to kill sandworms and cheering when they gobbled up my enemies units. Loved building bases in that game. My preference for more advanced RTS games though would be Empire Earth or Total Annihilation, didn't find those nearly as annoying as some of the other classic RTS games, as I'm not much of an RTS gamer. I prefer turn based strategy generally and have to do some long hard thinking before getting any game that touts itself as an RTS (Did pickup Battle Realms a few days ago due to the novel setting and the interesting reviews).

I find most RTS games get boring for me, even classics like Starcraft. After playing through the Terran campaign I only got a couple missions into the Zerg and decided I was done; but, because it had such an excellent story I found some cheats to auto win or make myself invulnerable or something, just so I could watch the rest of the story segments. Had a similar problem with Warcraft 3, just didn't have the patience to keep playing over and over till I beat some of the missions. Age of Empires is a pretty good one though as it's single player campaign has a lot of interesting history mixed in.

Start with the classic, Command and Conquer. Great story, fun cut scenes, cool units, easy to play and a wicked soundtrack. Then follow it up with Red Alert which is just as good.

I would also highly recommend Starcraft, Warcraft 2/3 and Age of Empires 2. In my opinion RTS games were not as much when they went 3d but that's just me. :P

Go with the C&C series.
Both the first C&C and the first Red Alert have been released as freeware.
As far as both series go, I would stop with the 2nd game in both series.

IMHO the 2nd installment in both series were better. You should give those a try.
They're equally complex, but more fun.

I can't seem to find these freeware versions anywhere. I think that I'm gonna get the C&C collection, but it seems like lot of them are spin-offs (or they are just weirdly named). Does anyone know if the Generals games are any good?

Dune 2000