Most of them are for the purposes of RP conflicts.
For example, some pirates are in a tavern, and might want to have a fight break out etc. Or try to rough someone up and steal something they're carrying (followed by said someone's friends retalliating)
Generally, RP guilds have RoE (Rules of Engagement) active. Stuff like, no killing at the bank or afk, no looting, etc.
Generally, fighting is kept to organized events, or in relation to the RP currently going on. (So they don't kill each other on sight, just because they can).
Sometimes they state that combat can only happen with specific gear equipped (to give newer or less active players a bigger role).
The biggest thing with wars like this - always insure yourself. The 'enemy' guildmaster may recruit some guy who just wants to grief. Generally, such a player will be removed from his guild once you go to his guild leader, but it doesnt get your stuff back if he's stolen it.
I don't know all of the specifics, but talk to Hawkeye Pike (Captain of the United Pirates) for more info. He has a lot of experience with this sort of thing. Reading his travelogues website has a few examples of guild wars used in RP as well.