"The personal Reputation System is a way for players to earn reputation with different factions or groups within Star Trek Online. Its general setup is similar to the Fleet Advancement System - By completing projects requiring faction-specific marks and various other resources, the player can advance through five tiers per faction, unlocking new items and abilities that are specific to that faction or group."
Taken from Stowiki.
Now: Do I have to do the projects in order to gain reputation, or can I simply do the romulan missions etc to progress through the Romulan Rep system?
A contract is a contract...(but only between Ferengi).