We discussed various tie-breakers at Dice Tower. (Note: The goal of the tie breaker should be to be "fair" which I define as awarding the match to whoever would have won if the match was played all the way to a conclusion)
Various metrics were suggested including:
* Less damage - although this is simple, this tends to disfavor slow-starting decks and favor agro decks.
* Unspent spell book points (Sum of spellbook points of all cards still in the spellbook)
* Unspent spellbook points + spellbook points in play
Personally, I really like one person's suggestion for something to the blinds in poker. That is, starting 60 minutes into a match, the tournament director announces that during each upkeep, both players take a certain amount of damage. Five minutes later, the upkeep increases; five minutes later, it increases again. It keeps increasing like that until one of the mages is dead. If they die simultaneously, it's a draw.