Right - lets get all the non John programs all in one place for new people here. Only legal modifications, and only programs with links. Preferably software that only exists in this forum or close enough, there are plenty of lists around of every portable app.
QSClient - Putty, WinSCP, NXclient, Xserver, and lots others all in one program. Install on local pc, run it and choose install to USB stick. Awesome bit of software!
CCleaner Portable - Deletes all temp files and sorts out registry problems. This is a launcher for the program, you need to download the offical program and put it in the same directory as this.
What else? I can edit this post if there are anymore - these are the ones I found by looking through the forum though - I'm sure there are more...