Ever hear of thought-mapping? Rich Redman showed me an article on it back when we worked together at Wizards of the Coast, and I always found it helpful when I was trying to organize my thoughts on a large process.
Recently, I was designing a new dungeon-delve-style adventure, and I decided I wanted to have some specific set-pieces to act as thematic hooks for the overall adventure. But I wanted to tie them together on the map, which meant that I needed to decide at what point they would occur in the delve. After I made a list of all of these set-pieces, I started to sketch out a rough diagram of how to get to them from other encounters and such. Before I knew it, I had created this thought-map:

Pretty straightforward: The PCs enter at "Entrance," and then have an Encounter, after which they can move on to one of two Set-Pieces. Each of those has branching decisions, one from each of which can lead to a "back door" to the other. Eventually, the PCs' path leads back to a single point, from which they can again move into two more areas, and on to the finale.
Using this thought-map as a rough diagram, I can develop the basic map:

This one is unfinished, as you can see by the fact that I still have the thought-map notes on the lower right.
It's also lacking spaces between the various locales--partly because I only had a limited amount of space to design in, and partly because I'm planning on drawing out the final map using TileSystem. (If you use Dwarven Forge Master Maze, but haven't heard of TileSystem, I urge you to go download it right now.) After I recreate the map in TileSystem, I can easily grab entire sections of the map and separate them, to create more space between encounters, and to give the PCs more safe havens between fights, where they can rest, cast healing spells, and so on. Obviously, I also don't have the rough room descriptions marked on the map, because I may change my mind and move things around later.
My theory here is that, by thought-mapping my adventure, even on such a specific, small scale as a single dungeon, I can ensure that not only do I not leave out important bits, but I can also ensure that I create challenges for specific characters: traps for the rogue to disarm, monsters for the fighter to overcome, magic puzzles for the wizard to work out, and theological dilemmas for the cleric. If I know the PCs (as I do, in this instance), I can also design the adventure so that it presents them with challenges for the skills they have maximized, reminds them not to neglect important skills they may have minimized, and even provides them with information relating to their backgrounds. (For example, one encounter in here is going to be with someone the PCs have met in the course of the campaign; I've removed the name from the map, since I know they read my blog ...)
Ever done something like this with your adventures? (I know that James Wyatt did something similar in The Speaker in Dreams, for example.) If you have, drop me a line in the comments section, and let me know how it went! And, if not, give it a try, and let me know how it goes.
JD