Probably the coolest thing to do for a portable app is to make a portable emulator that would allow Linux to run in a window while Windows is open.
This would ensure that people using corporate or school PCs which may not be configured to boot from USB or CD/DVD drives would be able to run their favorite Linux (which for me is Ubuntu if that means anything) without messing with the BIOS settings on a computer which is not theirs.
I'm not sure if it's open source but I hear a lot about QEMU or something like that. I figure that could be a good place to start.
--Eric