I just want to sing the praises of TokenLab, by the way. It lets you generate super-useful Maptool tokens from Hero Lab stat blocks. They have buttons built in for practically EVERYTHING -- attacks, saves, spells prepared/cast, feat reference, the works. I no longer need to have umpty-dozen character sheet PDFs open all at once. It's made my life so, SO much simpler.
I also make heavy use of Photoshop for making custom maps. Maps take time. Lots of time.
So pre-made maps like the ones in Paizo's APs are dead handy. To get those out, I use Nitro PDF Reader. It has a very handy 'Extract Images' button, which will pull all of the images out of the PDF and dump them into a folder for you. Transparency preserved (where available) and map labels omitted (barring the occasional S for Secret Door, which are sometimes annoyingly baked into the image).
Those three tools are exactly what I use.
Plus Obsidian Portal to host a wiki and forums. (We play by post)