Up until 2.4, the only way you could get uncut epic gems was by raiding Black Temple or mining a certain node in Mount Hyjal. That's it. There were a few other epic gems that dropped in Heroics, but they certainly weren't customizable as the uncut gems are. Furthermore, in order to cut the gem, you'd have to have Scale of the Sands reputation, which again... would be Mount Hyjal rep.
With the latest patch, all of the gem cuts can be obtained by reputation with the Shattered Sun Offensive. Magtheridon drops a Black Sack of Gems which contains 3 epic gems. And finally, you can also purchase gems from a different Badge Vendor.
The Gem Badge Vendor
Once your server finally opens up phase 4 through daily quests, you can now work on the daily quest to open up the Badge Vendor that sells uncut, epic gems. For a mere 10 Badges, you can purchase a nice, shiny, uncut, epic gem. (Edit:) This quest is called Discovering your Roots, and it can be found in the recently reclaimed harbor Inn. The quest requires you to go back to Shatt, fly NE to an elevated part of Terrokar Forrest to gather some roots. Pretty easy and straight forward.
So please, don't just focus on the Badge Gear Vendor. There's more to the Shattered Sun's plot to equip us all than that. They also want to make our gear the best it can be via these upgraded gems. So, get out there and do the dailies that will unlock stuff for your server AND for YOU!