choices and consequences
Blackwood company
Origin of the mages guild
Knights of the white stallion
Mannimarco resurrection light and dark (you can choose to stay with mages or side with the necromancers after the original quest line is over)
Integration ............. <_< >_> (not directly related, it adds 5 new guilds and a lot of its quests have faction checks for the original guilds)
Still think I'm forgetting one.