Factions

[yerkyerk]

You could, ofcourse, just disable the ability for players to do certain quest. Than they can join the player who gets the quest, but they won't get the quest reward or dialog if they have a different faction.

Still, I'm not sure if that's such a particularly good idea.

[Llama8]

Or have the faction-based quests dependant on the character that started the server & not give anyone without the required faction the quest rewards as Yerk said.
Or just disable them in MP (or enable all of them in MP).