Many Programs need to access the registry in order to run and that could be a problem. Why don't you make Wine from a Portable Linux emulator and then, people could have many more apps as Portable apps, or better, just make a portable Linux emulator and the users can do the rest themselves. 
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Wine Portable
October 4, 2011 - 8:49pm
#1
Wine Portable
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Wine doesn't run under Windows and many apps don't work under Wine. It's got bugs that affect everything (including some visual issues in the PA.c Platform). Linux in a VM running from a portable drive is very slow. Unusably slow in many environments.
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