One of the things I have done religiously while creating my Dwimmermount megadungeon is abide by the rules presented in Volume 3 of OD&D for the distribution of monsters and treasure. There are several reasons I've done this, but chief among them is that these rules ensure that about two-thirds of the rooms on each level contain no monsters. That means, for example, that of the nearly 70 rooms on the first level of Dwimmermount, only 23 of them will have occupants.
That leaves 47 "empty" rooms for the characters to explore. Of course, a lot of these other rooms aren't really empty at all, since they might contain tricks, traps, clues, unguarded treasure -- 1 out of every 6 unoccupied rooms has it according to the rules -- and just plain inexplicable things. My experience over the last 18 months of running a megadungeon-centric campaign has been that it's often the "empty" rooms that are the most memorable, as it's here that the players, through their characters, interact most immediately with the game world. Furthermore, empty rooms help build tension and mystery, both of which are vital to the long-term success of a campaign.
Dungeons & Dragons is, after all, a game of exploration. Dungeon delving is a quest for loot and knowledge and, far from being the focus of the game, combat with the inhabitants of the dungeon is but one possible obstacle standing in the way of the characters' goals. That's why it's important that dungeons, especially megadungeons, have lots of empty rooms. It's a practice I fell out of over the years and whose importance I only understood fully as I immersed myself in OD&D. Now, it's hard to imagine stocking a dungeon that isn't mostly "empty."