Whenever I reinstall an operating system, there are several programs I must install before I even think about developing.

Windows:
TextPad - The best lightweight syntax-highlighting editor I’ve seen for windows. Has all the basics and then some.
Cygwin - The basics of Bash on Windows. Write an honest-to-God bash script on windows. Never mess with a .bat file again.
Flex Builder (if I’m developing in Flex) - Self-explanatory
IntelliJ IDEA (if I’m in Java) - Self-explanatory
Innotek VirtualBox - 90% of the features of VMWare Workstation (and growing), at 0% of the price.
Maven (1 or 2) - Why would I ever want to learn how to use javac?
Python interpreter - Just a huge improvement over the default calculator. Sad, I know.

Linux:
Bluefish - Essentially the Linux equivalent of TextPad. Good for files that are a bit large for VIm.
IntelliJ IDEA
Innotek VirtualBox
Maven (1 or 2)