I would like to know, if I use WndProc in my C#.net app to handle minimize event in my form, will there be any problem if my app will be installed in different version of windows or other platform? like xp, 2k3 and so on?
Unless you do it wrong, no.
Native C apps work the same way, and they work on all versions of Windows (assuming that they are written correctly).
In general, if you go beyond WinForms and start using WndProc or Win32 API functions (P/Invoke), I recommend that you read Raymond Chen's blog, which describes many common pitfalls when working with native window methods.