I usually only keep 10 or so stacks of each gem, but here's what I use them for:
- Perforator to sell/DE
- Monocles of various colors, slow selling, but people do pay for them
- 365 epic weapons: I occasionally sell one on demand, I never stock them for any reason. I cannot fathom why people buy them, they aren't even cool looking.
- Cut random gems on demand
Unfortunately, Blizzard kind of forgot that those have zero value. The biggest reason I still keep them is the fact that eventually Heavenly Shards and Maelstrom Crystals will be nearly impossible to find, and most people still want to use the Power Torrent/Landslide enchants for leveling alts from 77-90. Having an easy supply of shards when I need it is worth keeping some to me.