Dungeons are easy to include once you get into the mind set of them. I personally use the term "dungeon" much in the same way as the new MMORPG community seem to use the term "instance". I.e- "A self-contained area in which a task of significance takes place".
Being self contained means you can plan out a lot more, and it means things have to be done in the order you want them too (although players have a tendency to skip things you hoped were unskippable anyway, had one group scale the walls of a castle to talk to a king, instead of making one bloody diplomacy check after a simple gather information check, but nevermind, its more interesting that way anyway)

When viewed this way a classic cave or underground labyrinth is a dungeon just as much as castles and keeps are (yes quite commonly used also),
but also just as much as a city (or section there of, like sewers or slums),
or a church (catacombs/wine sellers, even the church itself if there are enough undead outside),
or a courtyard (hedgerow mazes and animated plants are fun),
or a river crossing (with bridges/caves/cliffs/rapids/sink-holes/deltas which require lots of coordination to traverse safely, often with water elementals or amphibious creatures, if you've got a lot of height then sometimes flying creatures too),
or a wizards tower (wizard can be dead or not, still going to be interesting),
or metal works (large complexes with air-vents and forges and possibly mines nearby/attached to make for interesting layouts and fun locomotion at times),
or a ship (pirates anyone? maybe just retrieving an item which involves getting to a secluded floating craft and on board),
or an academy (mad apprentices, experiment gone wrong, retrieving research without being discovered),
barracks (easy to formulate things there),
villages (yes, they are dungeons too at low levels (preflight), more so if the inhabitance don't like unwelcome guests or do a lot of animal trapping),
etc...

The list goes on, a dungeon is anything that you can draw on a map and not have to worry about what's outside of it as it doesn't play a role in what's going on. Watch horror films for classic examples of potentially deadly areas people get stuck in, action films for how to keep people from leaving even if though they other wise could (think Die Hard here), and of cause adventure films for interesting locations and reasons for them being there.

Planar travelling is a good way of creating "bubble" universes too, as you often want to get in and get out and so there is little else to distract the players with, its also easier to keep players in line when they get to higher levels (never have my group ever regretted selling a "useless" item quite as much as when they sold the Boots of Walking I gave them. Just to find that they were the only thing they could use to get around an air plane they needed to go to because they allowed normal walking even in extremely high winds. A condition they had not expected when they had identified the item and glared at me for giving them such a clearly useless item but it meant I didn't have to worry about my warlocks 24/7 flight while they were there.)

Dungeons are basically an excuse to plan things out in more detail and not worry too much about rail-roading your players as they expect it (and if they are worth their salt they will get around anything you throw at them in ingenious ways you'd never even considered possible).

So go mad, not every dungeon has to be underground or classically trapped to the back teeth, think about the function of any place, and then think of a reason why the players have to go there. Even if its just a case of it being in-between position A and B (hell, there's that classic level 1 dungeon where your in a storm shelter weathering out heavy rain and you stumble across stuff of interest), don't be afraid to make them short lived, as long as its a challenge that gets your players thinking and lets them sink their weapons into some unfriendly's they'll be happy, I guarantee it.