Puzzles!

I love puzzles in dungeons, but I don't get use them as often as I'd like. Here's why:

1. Crafting a good puzzle takes time, and I have a terrible habit of not planning my sessions in very good detail. Often “session notes” consist of a few frantic pencil lines on a single notebook page. Puzzles don't play well with my largely improvisational GM style.
2. It's hard to find an excuse to include a puzzle. This is what drives me crazy about games like Prince of Persia or Tomb Raider: castles and catacombs seem to have been designed specifically for acrobatic protagonist puzzle solvers. I never put in a puzzle without spending some time thinking as the builder: who was this puzzle meant to allow in? who was it meant to keep out? What bizarre mania or lavishly excessive Evil Lair Budget drove me to build this thing?
3. Players might not think of the same solutions I do. In fact, they may not think of any solutions at all. A seemingly unsolvable puzzle is one of the most frustrating experiences in role playing.

Also, a lot of the puzzles you find online are pure logic:  anyone, PC or not, will be able to figure out how to measure exactly 5 ounces of magical goo using only a 9 ounce and a 2 ounce vial, but to me the best puzzles are the ones that require that the players have been paying attention to your world, your story, and their surroundings.

My general approach is to give the players the answer to the puzzle long before they encounter the puzzle itself. Give the PCs a symbol or metaphor that's important to the dungeon (secret cults with esoteric symbolism are great puzzle builders), and then later give them an obstacle that relies on that knowledge in a non-obvious way. Essentially you want to give them the key to the puzzle early, and you want to hide that key in a giant pile of fluff, flavor, and red herrings. 

Here are three of the puzzles I've created over the years:

Light Puzzle:

• Room 1 of the ruined temple has a massive ceiling mural showing a goddess bathed in yellow light.
  
• Room 4 contains a statue of the same goddess and a series of magical lanterns that each, when activated, fill the room with colored light.
  
• If the party activates the green and red lanterns (creating yellow light) the door opens. Any other activation of lanterns springs some kind of trap.
  

Clock Puzzle:

• Room 1 of the barrow contains bas reliefs resembling tarot cards, with numbers and names under each one written in the cultists' secret language. Many of them are ruined, so the PCs can only fully see four. They are: II- Rest; XI- Eternal Night; VII- Hope; IV- Slaughter.
  
• In Room 4, there is a giant clock. On the door to the room is an inscription:
  Here the dead their hours mark. Lay hands on hope, fear not the dark.
  
• Inside the room, the walls are filled with corpses. The clock is set to 2 o clock. Every time a PC takes a step in the room, the clock ticks forward and the corpses become more restless.
  
• The PCs need to turn the clock all the way back around to 7 (Hope) before it gets to 4 (Slaughter) and they get massacred by the undead. PCs will likely be wary of setting the clock to 11 (Eternal Night) unless they pay attention to the inscription.
  
• For added nastiness, the clock has a Dominate Monster effect on it such that the first creature within 30 feet becomes compelled to move the hands forward. It's no fun if the PCs have all the time in the world to concoct a perfect plan.
  

Armor Puzzle:

• The party is trying to retrieve the legendary armor of a dead king. The armor was split between his two sons, who each wore parts of it. The npc who tells this story makes sure to mention which son wore which parts, as well as telling what weapons the sons used and how they died.
  
• In the final chamber of the tomb, there is a mannequin with the armor on it. Two skeletons lie in open sarcophagi, each obviously killed in battle.
  
• An inscription says: If you are friend to these men, and would take their armor from this place, give first to them what was theirs. Else beware, for the land will guard you as it guards them.
  
• The party must discern which corpse was which brother, and give them their appropriate armaments.
  

These puzzles might seem obvious, especially the second one. Remember that the party has been through other rooms of the dungeon, each with its own challenges and encounters, so that the "key" is something that was a few hours back in session time, at least.

These puzzles also might seem cruelly challenging, especially the third one. Who seriously remembers which guy wore what armor? I was entirely prepared to let the characters make intelligence rolls to see who remembered what, and let them argue about their differing memories... but the alchemist's player rattled off the list with no problem at all, put the armor where it belonged, then when I told him that the tomb was appeased and the bodies crumbled to dust, the party walked out feeling like they had really accomplished something cool.