Wow, what a great thread!
So as GMs we've been running games a while, and we've made tons of dungeons before. But while some of these are super inspiring, I have a couple links to add for on-the fly dungeoneering. I find the hardest thing for me is to have nice, pretty maps for consumption so I have a couple links I use (and usually have a few different maps printed out in my folder just in case the players decide to spelunk, visit barrows, or raid an ancient evil temple).
My two personal favorites are:http://donjon.bin.sh/dungeon/
Nothing like having some sweet maps to put on the table to represent where you are. Both have the print-to-pdf capacity, and work great. The latter has a bit more drag and drop, but takes a while to learn and get the setting right. The first however doesn't have nearly as much customizeability or bizarre (but awesome) tiles you can slot in for just the right amount of lava or whatever random thing you want.