Dark Age of Camelot had three realms fighting each other in RvR. World of Warcraft PvP and Warhammer Online: Age of Reckoning RvR only have two factions fighting each other. A two-sided war makes for easier lore of the "good vs. evil" type. But as populations and classes in a MMORPG are never totally balanced, a three-sided war might be better to stop one side from dominating: The two others can always gang up on the one side that is ahead, and thus automatically balance the war again.
What do you think? Do you prefer two or three sides in RvR? Why?