My question was how can I store username/password PROGRAMATICALLY... not where can I download a tool that lets me do it myself one by one...
The solution is to encypt a password yourself and write it to an rdp file. While the current version of RDP doesnt create these files for you, they are still valid, and still work.
Details for encryption are found here:
http://www.remkoweijnen.nl/blog/2007/10/18/how-rdp-passwords-are-encrypted/