COMMERCE
Commerce amongst factions and any other groups or affiliations is a moderately simple procedure. When amongst factions the faction leaders discuss what they will be trading and what the costs are. Then they will trade the items. Since factions or tradeable items are far apart and the factions are normally busy doing other duties third party traders often handle the actual transport of materials/ships/resources/etc for a nominal fee. The common fee is a portion of dilithium (A single unit of dilithium can be divided into 10 dilithium chips. Typically, the fee is 10% of the overall cost of the transaction.
Any trade done between factions and non-player groups has to be cleared by a moderator, with the moderator taking part as the other party.
Just about anything can be traded, sold, or bought as long as a supply exists and they can pay for it.
In essence trade is an open option between factions and, when believed necissary, non-player groups. There are no real rules for what can be traded, so feel free to offer whatever you have at whatever price you believe fair to other factions. Just keep it within the Star Trek essence (No trading sentient beings, weapons of mass destruction, etc.)
Each empire receives income based on the planets and mines under its control. Within each empire, there are factions. These factions receive a portion of income based on their standing within the empire and how well they are achieving their goals. Within the Klingon Empire, these factions are the various powerful Houses, each vying for power and standing. Within the fledgling Federation in the aftermath of the Human-Romulan War, the two factions that have arisen are the militants - those who believe the Federation should be a strong power - and the explorer/diplomat/scientists, who want the Federation to be an altruistic, peaceful republic.
Though Klingon players may be a part of the same House, many will chose to form their own. Typically, a House has a leader that chooses how to use resources delegated to it. The two Federation factions are run somewhat like councils, with the resources delegated to each being decided on by the collective members of that group, though typically there will be one or two people delegated to doing this with the others simply asking for something here or there (since not everyone likes processing build orders and such.) Individual amounts may be delegated by the council/House to he players if the council/House so chooses.