I only recall various common gem vendors in BC, greens in limited numbers from Dealer Senzik in Netherstorm, and uncut epic gems from Shaani on the Isle of Quel'Danas for Justice.
In Northrend, I recall the only gems you could purchase were uncut epic gems from Harold Winston, the Jewelry Vendor and Legacy Justice Quartermasters in Dalaran and the major faction cities for Justice.
In Cataclysm, you can collect 2 types of raid tokens (Mote of Darkness from raid bosses, Essence of Corrupted Deathwing from Deathwing) that can redeemed from Dasnurimi for Geodes containing containing uncut epic gems.
In Pandaria, the only uncut gems that can be directly purchased are the Jewelcrafter's Serpent's Eye (actually a rare gem that become a epic Jewelcrafters Facet after it is cut) in exchange for a Spirit of Harmony. As of this post, there are no epic gems available in the expansion (with the exception of the JC facet cuts) at the moment.
I believe that the only reason the common gem vendors were available in BC was because JC was only recently introduced back in BC. But since then Alchemists and Prospecting have made gems to be more easily available, so there is no need to have these "entry level" gem vendors.
They also removed Gem Honor Vendors when Cataclysm came out.