PackageFactory is being used all over the web to get all types of apps onto U3.
Examples are many: you can download the popular Windows cleaning app CCleaner in U3 format so that you can fix up any Windows box whenever you have your U3 drive on you [U3 download page at CCleanerDownload.org].
PackageFactory for U3 lets you convert any* application or EXE into a U3P Package File, for free! You can then install this U3P file onto any U3-compatible flash drive.
PackageFactory for U3 is free to use for non-commercial purposes. The free version above has no restrictions and it will append "U3 build by Eure.ca" to the description of the U3P Package file.
To take full advantage of U3 platform the application you convert also needs to be U3-aware, or at least rely minimally on Windows Registry.