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.
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.
Sometimes, the impossible can become possible, if you're awesome!