...I'm stunned, a good question and an even better answer? Did I somehow enter the Twilight Zone of the forums?
Thanks for a very detailed answer that should help several people!
No problem, I try to look for legit questions on the forums and answer them when possible... they tend to get buried amongst garbage pretty quickly.
Edit: And more Specifically to the OP. Centurion Commendations (from champion bags) = tier 1 pvp, Champion tokens + commendations (from BM bags) = tier 2. BM tokens (no comms, just tokens from BM bag) = tier 3 pvp.
For PVE Tionese = tier 1, Collumni = tier 2, Rakatta = tier 3. Normal, Hard, nightmare operations respectively (crystals and commendations). You also get tionese crystals from hard mode flashpoints, you get commendations from doing weekly/daily HM heroic as well, in addition to weekly HM/Nightmare, Regular operations.