I have a handful of RTSs in my backlog, and I'm really in an RTS mood right now, but the problem is that I just can't decide which one to play next. I'm almost paralyzed by choice, it would seem. Anyway, here are the contenders:

Earth 2150
Earth 2160
Warlords Battlecry 3
KKND 2
Heroes of Anihilated Empires (Started this one a while ago, but got bored/distracted during the second level, so I never really got into it)
Tzar: The Burden of the Crown
Ground Control
Ground Control 2
Warrior Kings
Achron
Fleet Command (Jane's Fleet Command)
Theatre of War 1-3
Dungeons & Dragons: Dragonshard (played a little of this one, but it failed to grab my attention, never got far though).
Genesis Rising
Sub Command (I think this one's an RTS, not 100% sure though)
Alliance: Future Combat
BC Kings
World War 3: Black Gold
World War 2: Panzer Claws
Dawn of War 2: Chaos Rising (did not enjoy vanilla DoW 2)
Stronghold
Mosby's Confederacy
King Arthur 2
Joint Task Force
The expansions for Red Alert 1

Could anyone help me pick one?

You can get WW3 Black Gold working? I gave up on it.

ground control 1-2

Stronghold is a fun series! You can create your own castles!

Tzar if you want fantasy setting with standard mechanics, Earth 2150 if you want sci-fi setting. Ground Control in case you don't want to build bases. KKnD if youa re looking for big challenge (it's hard imo). King Arthur if you want something more Total War like. You should know yourself which way it draws you right now. :-)
Don't bother with Chaos Rising if you dislike vanilla DoW2. It's essentialy the same.

I would personaly go with Tzar.

Of the ones on your list, the ones I liked the most are Warlords Battlecry 3, Genesis Rising, Heroes of Anihilated Empires and Tzar .

Another vote for Tzar

Though I haven't got most of the titles on your list and I'm not the greatest fan of RTS game I found the Ground Control games rather good, although they are more tactical than strategical.
Initiallly I found the Earth 2150 games good but I never got very far in them before I lost interest.

I'm also curious as how Genesis Rising is, it looks a bit like Homeworld and could be fun enough.

From what I've read in the reviews, you can skip Ground Control 1 and just play the sequel, GC2. Personally, I've enjoyed GC2 a lot- the combat system is interesting, it's different from other RTS games in that you have to hold and protect key points on the battlefield, so it's not like you're safe if you secure them, I like that. If you care, GC2 also has interesting characters and storyline.

Didn't play Total Annihilation ???

Edit : my bad .... slow reaction from me.... this is your backlog, and you want advice for picking something out of it. Now that I read it, the only one in that list that I played (I played a little less than half) and have good memories of, is Warlord Battlecry 3.

Stronghold. It forgoes a lot of the annoying micro-management of other RTS games and it makes building your own castles very involved and rewarding.

Warlords Battlecry is a really fantastic series as well. I think WBC3 isn't nearly as good as WBC2, though.

I'll throw in another vote for Stronghold. I thought I couldn't bear to play yet another RTS with the same old subzero moronic A.I. but Stronghold is such solid fun in every other aspect that it's an absolute must play experience. Easy to get into, easy on the eyes and hard to put down.

So Tzard & Stronghold got exactly the same amount of recommendations, but Stronghold is higher up on one innerring's list of recommendations. Thanks everyone for helping an indecisive person pick a game!