You ask:
I am willing to re-write my best Windows software from scratch, but I insist that the result is native or almost on Linux so there are not any weird GUI glitches. Do you think Wine is the way to go for me, or am I better off writing individual versions and keeping the Windows software native and then producing QT or GTK versions for *NIX? I'm at a cross-roads here, since I'll be dedicating years of work in whatever direction I take.
IMO Wine is the perfect tool for you. We know, it's not perfect. But the best use of your time (and the most efficient) would be to: 1. Fix any problems in your apps (like reliance on strange Windows corner cases, use of very obscure features) 2. Help out fix Wine so that your apps run properly.
This will not only help us a lot, but it will help you make good use of your time, and it will allow you to do cross platform development (even for Windows) from your Linux box.
Please direct questions to wine-devel@winehq.org, where people can help you out.