Security for USB drives

I used to work in a university where malware was rampant on all the smaller local networks. I love the idea of my most,-used apps being portable on a stick. But I am a little worried about plugging a stick into a bunch of different computers. I would like to hear about people's experience with malware and it's prevention with portable apps. Also if Portableapps.com has recommended best practices for malware hygiene, I would be glad to know what they are.

Warmest regards, Andrew