I always start by thinking about a central theme and interesting encounters that I want to fit into the dungeon. I then design the lay out of the dungeon by thinking about what purpose each room serves. If the dungeon is home to intelligent creatures, then it should have rooms to fulfill their daily needs. Which means such rooms will probably have furniture in them, and maybe creatures going about their daily routine.
If the dungeon has traps, then there has to be a means for intelligent creatures to bypass the traps (unless the dungeon is uninhabited). Most of the time I will create an alternative path in the dungeon that bypasses the traps, or there will be a hidden lever/swith to deactivate the trap. I try to think about how these traps would function in any realistic sense. If the trap emits a jet of flame, then is this magical, fuel based or gas based? If any of the latter, surely there are reservoirs that can be refilled that are near where the trap is installed?
Another interesting thing to think about, is whether there are any unintended paths through the dungeon. Are there walls that have corroded with time? Do some of the intelligent monsters perhaps avoid parts of the dungeon that they have deemed unsafe? Have vermin borrowed through the walls, creating new tunnels? If so, maybe there are vermin opponents in some of the outskirts of the dungeon in addition to its normal population of bad guys. Can the players break down some of the walls with explosives and/or spells to create a shortcut? By giving some of the spaces their own story, this can inform where the monsters are, and where they are absent.
I also try to add obstacles in the dungeon that provide an exploration challenge, and require the use of certain skills. A weak floor may require careful movement, a collapsed stairway may require climbing, and a flooded passage may require swimming. Dungeons are often dilapidated structures, and parts of them may have broken down over time.
In my opinion it is just as important to add alternate paths in a dungeon, as it is to eliminate pointless filler space. I try to condense the dungeon in such a way that every space in it serves a function. If there is nothing to be done in any room/corridor, I either find something to put in it, or I eliminate it all together.