Adobe Acrobat 8 Professional -- viewing and annotating .pdf files
Adobe Photoshop CS3 -- editing images
CPU-Z -- if you need detailed information about your computer hardware
Dropbox -- for cloud storage
Eclipse -- for writing Java programs when necessary
Google Chrome
Graphmatica -- for graphing
MATLAB -- for modeling and graphing
Microsoft Office 2007
Microsoft Visual Studio 2010 -- for writing C++ programs when necessary
Mozilla Firefox -- most frequently used add-ons include Zotero, Tab Mix Plus, LastPass, Adblock Plus, Fasterfox Lite, HTTPS-Everywhere, and Lazarus Form Recovery
proXPN -- if you need a VPN
Sophos -- antivirus software
VLC media player -- plays almost any media file
WinDjView -- viewing .djvu files
WinRAR -- for zipping and unzipping compressed files