These are some things that I try to include in every dungeon or de facto dungeon. I don't always succeed, but it's handy to have them all typed out.
Theme: Each dungeon should have a theme. Sometimes it's locational, like "we're underwater" and imparts a sense of direction to the dungeon rooms. Sometimes it's strategic, like "if any fight lasts longer than two rounds, the monsters in the adjoining rooms will join in" to make the way the party approaches the dungeon fundamentally different.
Boss Monster: A climactic fight that will serve as the dramatic capstone to the dungeon. It is not necessary that the players clear every room or whatever, before hitting this.
Mini Boss: A second boss creature that needs to be killed to get to the main boss, or that is optional and gives extra treasure.
Saving Throws: Something should be included that targets every saving throw. If shy a Fort or Reflex save, I can usually add a trap. If I am shy of Will saves, I can add a boss aura that causes fear or otherwise needs a Will save to negate. Additionally, if there is only one or two instances of a particular save in a dungeon, I tend to make those saves more important.
Environmental Hazard: Something that makes fighting in that area different or dangerous. A ledge, a pit, a pool of acid, wind that pushes the players and hinders ranged attacks, whatever.
Outre Battle: An encounter that will overmatch the players if approached without imagination or advantages. This should be fairly clear to the players before the battle begins, if you want to be nice, or it can become clear after the fight starts, in which case the players should probably work out a retreat or other alternative strategy.
Reinforcements: An area whose inhabitants reinforce the other major battles in the dungeon, but that will stop reinforcing when cleared.
Puzzle or Problem: Something that can't be solved by a die roll. Bitter experience has taught me that failing to solve these should not be a hard stop, but rather should make things more difficult or deny the players some advantage. Usually, the advantage is treasure or information.
Jalea Acta Est: Some kind of item or shrine that offers a permanent, random modification to a character. Things on the result chart need to be weighted so that there is a really slim chance of something horrible happening or only a moderate chance of something annoying happening. This is one element of old-school D&D that I definitely like.
Cursed Items: The "you must use this for x sessions or x levels" way of working cursed items is really great, as is the "it's almost worth it" method of cursed item design. I think cursed items should ideally offer something that is not normally available to a player, but at some terrible cost that makes the character dangerous to others and himself.
Minor Resource Conservation: This is something that I oscillate on. By shifting to per encounter abilities, things have definitely moved away from the old resource conservation aspect. Hit point totals have also been more or less easy to keep filled up. This is nice, because the "i rest after each fight" thing was horrible. The thing is, it's hard to view a dungeon holistically if there is so little carry over from each fight to the next, and including things like vile damage or lasting debuffs only seems to aggravate players. Still, it is sometimes worth having a couple of traps in the dungeon with penalties like "if you fail to save against this pungi stick then you are slow during the first round of each encounter for the rest of the dungeon" and so forth. If I wanted to return to some element of resource conservation, it would not involve conservation of offensive abilities like daily spells or maneuvers, but rather some kind of HP based thing where players were limited in how much they could heal. They should reach the boss with a little wear and tear, I think, and should be punished in ways other than just losing party members along the way.
Aura: At least one monster should be dangerous to stand next to, in order to give reach a reason to exist.
Diverse Tactical Situations: I like alternatives to the "kick in door, kill everything" motif. Things like a fighting retreat, or defending a central point with a map of the area provided, can be fun. As can rewarding speedy dispatching of foes. As can splitting the party up with a falling portcullis, slide trap, or teleport trap. This last one is really fun, actually, because the game is so teamwork oriented. I guess it is sometimes nice to see what the characters can do on their own, under adverse circumstances.