Exploration Points (badges of orders 2nd, 3rd and who knows what)
Space anomalies and junk you loot
Personal shield buff things that can be turned in to upgrade gear (WHA?)
Some say this is to prevent credit farmers on day one and to make the currency have more meaning but the game is all over the place with skill points and currency if you ask me.
I do not know for a fact what badges of exploration are for because they are not active in game right now. I would assume, true to their name, that they are for exploring. There are badges of the 2nd order, 3rd order, 4th order and maybe some more but how they are gained? No idea. Add to that the fact that the Klingon side is woefully incomplete and these badges seem to create more headaches than solve them. I quote:
I finally found a dev to tell me the way to get "Badges of Exploration" is to do Star clusters (Genesis/Exploration system). The problem is that Klingons don't have access to Star clusters so we have no way at getting the badges. Please replace all Exploration Badge items with PvP Medals until you give Klingons Star Clusters
Then we have Starfleet Merits. We have energy credits. We have pieces of junk that we pick up and can use to upgrade gear if we turn in a certain collection of them.
The currency in this game is all over the place. To top it all off the PC skill points and bridge officer skill points are not given out at the same rate. When you complete a mission in this game the list of stuff you get scrolls like credits at the end of Avatar:
You have gotten bridge officer skill points!
You recieve Starfleet Merit points!
You get XXX credits
You get some random gear thing that may or may not go on your ship or crewmembers
You have looted a space anomaly or some debris thing
You have gained a level in our obscure bloated leveling system (level 3 first commander of a 2nd platoon!)
Too much. Add to this that each currency type has a vendor and you are running all over trying to figure out what to spend where PLUS you can buy ship modifications and change the way things look. So that is another vendor for cosmetic purposes only.
If anyone in beta at this moment can clear this up for me feel free to post here. Until then I am going to scour the STO boards for a definitive post on this and then cut and paste that sucker for long term reference. I could RTFM too but I doubt it is in there. Good luck asking in game. Zone chat is full of arguments about WoW, Star Wars Galaxies, people asking where to get a light saber and others proclaiming that EvE Online "sucks compared to this game".