How about scoring players for completing a dungeon, with the score being converted to tomes?

Using Castrum as an example, which currently gives 100 tokens:

Standard completion: 80 tokens
100% exploration: 30 tokens
50% of enemies defeated: 10 tokens
100% of enemies defeated: 40 tokens

Of course, the rewards would have to be altered to include more bonuses, and the actual numbers would probably have to be tweaked, but something to encourage players to really play through every bit of a dungeon while giving them adequate rewards for it would probably go over well.