I'm working with Tk under Linux as well as Win32, and while not always easy, I found it a better option than Win32::GUI. Why?
Like Chmrr says the documentation: What I did with Win32::GUI was hardly documented.
Stability. The things I tried in Win32::GUI were very unstable and crashed more often than Windows itself ;-)
Tk is portable. I run the same code on Win32 as on Linux. With NO change. There's not even a single command I have to keep in mind that does work on one, and doesn't work on another platform.
But of course there are a few advantages of Win32::GUI too:
Real Win32 gui elements. Tk comes from the X-environments and the look and feel is not 100% Win32...With Win32::GUI you're accessing the real Windows-controls
If you're familiar with windows-programming at all (like in VC(++) or VB), it is probably easier to use Win32::GUI in Perl.