I thought these apps may be good for inclusion in the portable apps suite.
These work with Windows and Linux (wine) with little modification:
- WinSCP http://winscp.net/eng/index.php
- mutorrent (not open source) http://www.utorrent.com/
- Portable Tor http://sourceforge.net/projects/portabletor/
The privoxy package that comes with PortableTor doesn't work under Linux for some reason but it isn't strictly necessary for PortableTor to work.