(Cobbled together from Torhead, the SWTOR forums, dulfy.net, and personal experience; ordered by quality/how you can get them.)
Standard
Green items. Requires low-level artifice to craft (items at level 7 and above); found in standard weapons.
Prototype
Blue items.
Artifact
Purple items.
All the above (Orange level 50 schematics drop from the Primal Destroyer world boss on Belsavis)
Magenta, AKA "Light Red" (must be crafted; not to be confused with Purple)
Black-Orange (direct from PvP vendor and also drops from Operations; can be RE'd for schematic)
Black-Purple (direct from PvP vendor and also drops from Operations; can be RE'd for schematic)
PvP
Cyan, AKA "Light Blue" (PvE versions found in Operations; can be RE'd for schematic and Expertise schematic also drops from Grade 6 PvP crafting boxes)
Purple (PvE versions found in Operations; can be RE'd for schematic and Expertise schematic also drops from Grade 6 PvP crafting boxes)
Black-Red (direct from PvP vendor and found in Operations; can be RE'd for schematic)
Black-Blue (direct from PvP vendor and found in Operations; can be RE'd for schematic)
Special
Razer Black/Green (for buying a Razer SWTOR peripheral)
White (world boss drop during beta; sold on the fleets prior to Patch 1.2; now drops from Cartel Packs and can be sold on the GTN)
Pink-Purple (drops from Cartel Packs and can be sold on the GTN)
Cyan-Blue (drops from Cartel Packs and can be sold on the GTN)
Orange-Red (drops from Cartel Packs and can be sold on the GTN)
Lime-Green (drops from Cartel Packs and can be sold on the GTN)
Derelict-Purple (drops from Cartel Packs and can be sold on the GTN)
Black-White (drops from Cartel Packs and can be sold on the GTN)
Silver-Blue (drops from Cartel Packs and can be sold on the GTN)
Orange-Yellow (sold individually in the Cartel Market and can be traded)
Discontinued
These are still in the game but can no longer be acquired if you don't have them already:
Black-Yellow (for pre-ordering the game)
Black-Green1 (Rakghoul Outbreak world event rewards. This is a different color than the Razer Black/Green, see this image)
1The Black/Green crystal is Bind on Equip and can still be sold on the GTN if the owner has not used it, so technically you can still get one.
Unavailable
These are part of the game assets but have not been made generally available: