Microsoft Excel: For making lists of encounters and loot when generating scenarios. Also for Simpson's excellent Mutants & Masterminds character sheet!
Adobe InDesign: For any sort of page-layout or word processing (scenario outlines and player handouts). I also make 4x6 index cards of every character, NPC and monster.
Adobe Illustrator and Photoshop: For maps and any other image work that I need to do.
Adobe Acrobat Pro: For creating setting info guides for players or posting PCgen characters online.
PCgen: For making D&D characters and NPCs.
Macromedia Dreamweaver: For campaign websites.
A Browser (usually Safari or Firefox): For the html version of the SRD and various online resources.