I received several notes that my original poll (here) was lacking viable options so I am resubmitting this thread.  A new and improved poll is on the way, and thanks to those who gave input in the original thread.

Of course I'm gonna suggest a 7.62x39mm A2.

But a better description of what you intend to use your upper for would help.

the 7.62 variety I'm also considering but I'm having trouble justifying it to myself.  As for what I will use this for - well, I figure if I build a .22 LR rifle it would be my training and "stray cat" rifle.  If I go this route I'll get a suppressor for it.  If I build one with cartridges larger than 5.56 I figure I'll use it for longer range target shooting and I would also use it as a hunting rifle.

You can just get a Ciener kit if you want to shoot .22LR with your AR.

Based on the avaliability of the ammunition argument, I would suggest 7.62x39 but it seems more practical to just get a SKS or an AK when you weigh the costs and benefits.

For another AR upper, I really like the 6.8SPC and .458 SOCOM.
There are quite a few different loads avaliable for them and they are both much more impressive than the standard 5.56mm cartridge.
Avaliability isn't an issue to me since I reload but the gist of it is that most ar variants or custom uppers are specialty builds for specific tasks or purposes.

What do you want to do with your rifle? That will determine what your cartridge requirements would be.

If you just want to plink, .223 is suitable and is accurate out quite a ways. If you want more range, you can get a match grade full length barrel etc.
If you like precision and have experience with reloading or wildcatting you could go with something like 6x45 or another bench-rest oriented cartridge.
If you want a little more performance for hunting or what have you then 6.5 grendel or 6.8 SPC are good candidates.  
If you want to hunt large game with a big-bore AR the .450 Bushmaster, .458 SOCOM and .50 Beowulf come to mind.

7.62x39!  Fun& cheap to shoot, and it did the job quite well deer hunting the last 2 wks.  

My vote, is for the 7.62x39.  Good selection of ammo, common and available in the U.S., still cheaper than most, and accurate enough, in the ar15 platform.  

Hand loads are also doing well in the accuracy and game taking elements of this cartridge.

Deer taken at close to 300 yards with it.  Coyotes close to 200 yards.  Does'nt get much better than that.

Good close in cartridge.