PackageFactory for U3 is a tool that you can use to package your Windows application in a portable format for your USB device. That's the theory, at least. The problem is that it's quite tricky to turn commercial software in to a portable version as they rely on the host Registry and need to be installed on the system. Any app that requires minimal Registry intervention should be able to be packaged as portable version. This is free for non-commercial use.
PackageFactory for U3 link.
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