Well, you could have the Knights of Good vs the Axis of Anarchy.

(from The Guild, in case anyone hasn't seen it)
But seriously, I would first consider who's perspective the tale is being told from. On the States side of the pond, we call WWII belligerents Axis and Allies, though the naming could have been different from their point of view. So do you want to paint a certain side as villains or vice-versa with some nice propaganda?
And another thing to look at would be what the war was fought over. I know you said it's unimportant to your plot, but it would give some ideas for names. Was it a holy war? Fought over resources? A colossal misunderstanding? Pretty much you need to ask yourself what history would call these things, if they are indeed in the past to your characters.