I'd say the first step would be to pick a "common" monster around the CR level of the players that will encapsulate the majority of encounters in the dungeon. These are typically the "grunt" encounters of a dungeon, they exist to make the cool encounters that you plan more awesome by comparison.
The most important thing when planning grunt encounters is to introduce some kind of battlefield hazard or something that would inhibit the PCs and prevent them from breezing through an encounter, such as a narrow walkway they have to cross to get to the grunts, the tunnel the PCs are walking into ends in a huge pit where the grunts are waiting at the top of the pit, firing down on them. Etc.
Make your grunt encounters as interesting as you can despite being grunt encounters. Give the players a puzzle to solve while they're trying to fight them and the battle will seem more like a battle and less like a slaughter.
Can't spell slaughter without laughter
You're going to hit a time during a dungeon when you're doing things that aren't really major exciting and things are starting to get a little monotonous. This is where this part of the dungeon building comes into play.
Essentially the concept is this:
Take a group of enemies that would normally be a decent challenge for a group of your Player characters at their level and put the enemies in a position that is funny and build the encounter around this. A good example of this would be enemies inside of a room with a ceiling that is consistently raising and lowering every other round. In order to fight effectively the creatures have to squat in rhythm with the ceiling of the room in order to fight the PCs.
Of course the Enemies would know about the room enough to attempt to plan around it, but you could just as easily fill the hallway on the other side of the room with enemies and have them see the PCs and bust into the room, stepping onto the pressure plate whose presence they were unaware of.
Make a Big bad
Everyone knows what a big bad is. He's the champion. The hero. The guy who exists to make your PCs lives a living hell and he's got a head full of empty and an axe full of angry. He's got more HP than you can shake 1d100 quarterstaves at and enough Damage resistance to make the sharpest weapons cause nicks and cuts. Counterbalance the DR with low armor class and you've got yourself a boss.
This is the one aspect of the dungeon you don't wanna skimp on. Make a cool boss for the PCs to fight. Make a Minotaur dual wielding bright pink battle axes wearing a silly red bandana who does ridiculous kung fu poses between rounds for no apparent reason. ( Until you get him to less than half health and he goes into berserker rage )
Make the pink battle axes really powerful for the PCs level, but only if you soak them pink paint once a day. Make the PCs spend time each day dipping the axes in paint, and scraping off the paint for the prior day. Give the axes fanciful names and give them an ego to make the PCs do silly things in between rounds to retain their full enchantment bonus. ( A +5 battleaxe where you must dip it in paint daily and do a silly pose every other round to maintain its magical edge. Whimsyaxes. )
Come up with concepts and encounters that make your game interesting, funny, or compelling on multiple standpoints.
Create a trap with a ridiculously high disarm DC filled with "unknown" poison that spits out laughing gas and marbles if the rogue fails by more than 5 points. Animate the marbles to pool under the feet of the PCs if they don't fall in the first round.
Create an NPC pirate that has lost his peg-leg that has to be led through the dungeon to find the leg, and have him run from every encounter with one leg until you assist him in retrieving his leg, then have him come back near the end of the fight and state that its lucky the PC's have him around.
Fill a room with harmless jello and make the PCs make squicky noises whenever they have to move through the ooze, if they don't make the noises they suffer a 50% movement penalty.
You can make a game as interesting or as boring as you want based on HOW you build it, even if its filled with nothing but goblins. Want to give your worldview a huge turn upside down? Literally?
Take a dungeon generated on Donjon and use the map it generates as a SIDE-VIEW MAP. Suddenly the climb skill becomes valuable and each encounter has a degree of difficulty it didn't have before. Take your dungeon and ROLL WITH IT. Make it fun, make it exciting. Do things that will surprise the PCs.