Self-install (QUT MOE)
Adobe Reader X
Apple QuickTime 7.7
GPL Ghostscript 9.00
Matlab 2012a
MS Office 2007
MS Visual Studio 2010
SSH Secure Shell 3.2.9
Stata 11.2
VLC Media Player 1.1.11
Without admin rights
JabRef 2.8.1
R 2.15.2
TeX Live 2012 (with TeXworks)
Linux Mint Debian Edition (on a new partition)
Requires Administrator priviliges
Foxit Reader (but make sure it doesn’t install any crappy browser plugins!)
Intel Parallel Studio XE 2013 (Intel Visual Fortran 13.1 as well as C, C++ & MKL)
RStudio (a bit flaky, but useful)
Rtools216 (includes both 64bit & Win32 versions of gcc & gfortran)
Matt Moores 
Also add to this JDK 8u101 with NetBeans 8.1 for Win64: http://www.oracle.com/technetwork/java/javase/downloads/jdk-netbeans-jsp-142931.html
pandoc is useful for R package development:
https://github.com/jgm/pandoc
PuTTY might be preferable to SSH Secure Shell, especially if you need to use the same private key on Linux and Mac OS
http://www.putty.org/
WinSCP 5.9.2 gives a graphical interface for secure copy: https://winscp.net/eng/download.php