Beyond Compare (Costs Money/Needs Crack) - Smart File/Folder Comparison software, great for editing code.

irfanView - my tool of choice for batch processing of image files, mainly manga. Supports tons of image effects like croping, resizing, converting between types etc, also has a renamer. I primarily use it to protect the manga scene from idiots who think manga pages should be 2MB PNG's

Kraco already mentioned my most used program renameIt so I'll just second that. It's a great program, regular expressions are awesome and being able to apply multiple regular expressions to the same files is even more awesome. If any one is interested I even wrote a set of generic regexes for renameIt that converts most standard formatted anime release titles into "Title - ep - [Group]" so they'll sort by episode number instead of group in the event a series is picked up by several groups but you still want to archive it.

mIRC - Why isn't this here yet? mIRC is open pretty much 24 hours on my PC. It's useful for much more than just chatting. With it's built in scripting language it's great for getting files and information as well.