TrueCrypt is an free/open source encryption package... Encrypts the whole thumb drive or just a file that you can mount. Use it in traveller mode... requires that you are an admin on a windows system.
KeePass is a portable open source utility that can manage your passwords.
7-Zip is an open source file compression utility... you can zip/7z up a text file and encrypt the archive with AES256. Command line version makes it portable.
Gnu Privacy Guard = OpenPGP... you can encrypt your file and run it portably from the USB drive.
Steganos LockNote is an executable that is a portable text document... you can password protect the text contained in that exe file.
I could go on for a while, but the above should get you looking in the right direction... I'd say KeePass is your best bet.