Stag Arms builds a quality upper for a good price, so that is certainly an option. Rock River Arms (RRA) stuff is excellent and fills up a good portion of my BRD habits.
You really need to figure out what it is you want in your rifle. There are a lot of trade-offs between the 5.56/223 and the 6.8, especially when it comes to the cost of ammo and ease of finding it. I personally wouldn't recommend the 6.8, but that is my personal preference.
As for your upper...what do you want to do with it? Punch holes in paper/targets? Hunting? What range do you want to shoot your rifle the most? Do you want optics or just iron sights? Etc. All of these are important questions for you to ask yourself before deciding on what best suits your needs. You can go for something along the M4/carbine route with a 16" barrel, fairly lightweight, with a flat-top or an A2 upper. You can also go for a service rifle setup with a 20" barrel, rifle-length gas system, again in flat-top or A2. Finally, you can go all-out target and get a heavy bull-barrel setup with a barrel up to 24" in length. It all just depends on what your intended purpose for the rifle will end up being.
You should also look at the following companies for some good deals on quality upper halves for good prices:
Welcome to Model 1 Sales' Online Order Center
Upper Receiver Groups AR 15 (Bravo Co. has their own line of uppers, which are of very good quality for a good price)
Rock River Arms (RB Precision is a great place to get RRA uppers)