I liked the computer game Freelancer's method of your actions influencing your standing with the various factions in the setting, including the "friend of my friend" bonus or malus your actions for or against some other party would incur.
Keeping tally of that in the freeform environment of a GM's table is a bit harder, though, although that also includes the option of getting away with crimes by keeping the affected party uninformed about your involvement. (Performing a hit job for another faction will sooner or later leak from the organization paying for the hit job.)
What exactly does joining a faction mean? Taking a vow of service, or just aligning your current business model with that of the faction in a mostly mutually beneficial way?
Getting a say in a faction might come through indirect methods (placing assets, lobbying, bribing, re-organizing character or actual assassinations) and means a fair bit of book-keeping to keep the revealed and un-revealed actors in the faction organized and up to date for the GM and the players. In settings with significant communication delays, local chapters of a faction may have rather different agendas or at least priorities than the main faction.
