One common criticism of Wizards' D&D 4E dungeons is the lack of "empty rooms". Empty rooms are supposed to provide both flavour and a time sink so the DM can roll for random encounters if the PC:s waste time searching unintelligently. Random encounters were taken out somewhere around the 3:rd edition of D&D, but flavor is still a worthy reason to put in empty rooms.
Verisimilitude is a good reason too. Especially in D&D 4E, where there are fewer encounters, empty rooms are ofter a useful way to flesh out the dungeon without adding much effort in creation. Of course, they may still be used - as storerooms and the like.
Of course, if one grabs existing maps, the empty rooms probably place themselves. Consider this map from Wizards' Map-a-Week. (The Dungeon Level in Expedition to Undermountain, supposedly.) If one were using this, one'd probably just place encounters in a tenth of the rooms and leave the rest empty. Gives some perspective to just how big it is compared both to the party and to the inhabitants.
The other approach is of course to have an abstract dungeon. It's implied to be a vast network of caves, but only the places where anything happens are mapped, and navigating the rest is handled by skill checks. (Dungeoneering to keep your bearings, Perception to avoid roaming monsters, etc.)