1. What exactly is the scope of things? What does the dungeon look like with nobody inside it? Is it all made of brick and mortar? Is it rough-hewn stone. Is it in a cave? Is it made of wood? Does it have flowing lava everywhere? Firebird says it best, "Know your surroundings." This avoids the disjointed feeling players may get going from room to room. Make sure it's not constantly changing based on your mood.
2. What kind of challenge will this present? Try spacing out the difficult battles in between some smaller cronies and henchman. If every dungeon progresses in the "ladder formation", then players may start feeling the snooze fest. This is part of making the dungeon part of your living, breathing world. The creatures of this place don't just freeze when the heroes exit. They were doing what they were doing before the heroes decided to enter. This one little detail can make or break your game, as small details can keep players interested in what happens around them. Also, think of the flow of the dungeon like a house. Does it loop back into itself, like Skyrim? Does the cave come to a dead-end? Is it just a big warehouse?
3. Now you can worry about what enemies to put in. You've established the surroundings and context. You've established the map. The last detail is filling it with your enemies. Now it may be tempting to throw in everything the DM thinks is awesome, but don't rush! Just keep in mind what was in the room before. Don't have killer fish-men in the room right after a mutant bee-hive filled with lasers. If you want to have fish-men, just have other things appear in the dungeon that may appear with fish-men. Patience, patience, patience!
*Bonus XP: To give your dungeon a bit of familiarity, play a game of classic Clue. Each of the rooms in the house has a certain context within the goal of the game. Sure, there aren't any monsters in the house, but there also aren't any inexplicable changes in scenery to throw players off. The whole scene is tied into the ultimate goal: solve the murder. Keep the players playing the same game together!