IMHO it isn't a problem. Personally, I never use Wine, or anything Windows-related. If I wanted to use Windows-applications, then I would not use Linux but Windows. I think you should see if you could find a Linux-application which looks a little like the one you had on Windows, and then use that application, instead of emulating.
Yes, Wine supports registry keys.
Edit:
I found two useful links about Wine and registry keys.
http://wiki.winehq.org/UsefulRegistryKeys
http://www.winehq.org/site/docs/wine.../using-regedit