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well the wine project is the most likely way to do it, but i wouldn't really hold out much hope if it's pretty obscure software which has close links to hardware too.
If wine doesn't handle the executables, then you could try with some CodeWeavers tools. Maybe they have something for such issues. This depends entirely on the executables. You have a lot of testing and research ahead of you.
are you just wanting to encrypt the file systems? or are they already encrypted?
i'd say drop the exe based software and focus on free software for it. i'm not trying to make you lose hope, but likely there is something free and open that runs in linux that will do just as good of a job.
a really common tool used to encrypt stuff on usb keys is truecrypt. if that's what you're using, there is a linux version available. you can download .deb and .rpm packages from www.truecrypt.org.
If you have a U3 flash drive like the SanDisk Cruzer then it is not compatible with linux or even OSX. As suggested your best option might be to remove the U3 stuff and use something like truecrypt.
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