When I'm designing a dungeon, I produce my documentation so that I can run it using three documents. These documents are a map and two spreadsheets. The first spreadsheet covers random encounters (and traps), the second covers the rest of the dungeon. I'm going to discuss producing and using the second spreadsheet in this entry. This may be mainly of use to new players rather than experienced ones.
I draw on two of Courtney Campbell's documents for my random generation needs: Tricks and Treasure. I also draw extensively on the AD&D 1e DMG's random tables. These are the actual engines churning underneath producing specific outcomes, what I'm discussing is how to document these decisions, including what data is most useful to include and how to structure it to be concise, consistent, and easily referenced.
Here's the layout I use. This is a selection from a real dungeon I ran players through. "OB" is short for "obols", the standard currency in Necrocarcerus.
When I'm filling this out, I start by rolling for the contents of each room - what combination of traps, monsters, treasure, etc. does it contain, and I mark each one with a "x" until I come back and fill in the entry. For monsters and traps, I mainly just use the random encounter tables I mentioned above, unless I get my interest piqued by a specific monster or puzzle. I use the "Special" column mainly to note linkages between rooms. i.e. "So-and-so's quest leads here" or "The key from Room 14 opens these doors", or weird exceptions like "Impenetrable glass doors" etc.
I use this format because it's built around making the information easy to reference in play, whereas I find traditional adventure layouts tend to bury this stuff in longhand paragraphs. The categories match up exactly with the generators I use, allowing me to rapidly generate and sort information, as well as track it during the dungeon generation process. If you haven't tried using something like this to organise your dungeon information, I strongly recommend giving it a try and seeing how it runs for you during play.