The best for Web applications on windows is, I think, the Cygwin's Perl. I was much impressed of how smooth the fork()ed loaded application works in FastCGI ( FCGI::Spawn, FCGI::ProcManager, etc. ) environment and, probably, the same should go here for cygwin's mod_perl against any other mod_perl.
But to write the desktop applications with WinForms, etc. my personal choice is the ActiveState's Perl. I find it easy with WxPerl to provide the compiled binary for the plain Windows user. ( WxPerl uses native forms for windows, same should go here about Tk and Gtk Perl bindings ). You may do desktop applications with Cygwin also, but this should require the ( Cygwin's ) X server on the client, which may appear troublesome for the end user and less efficient in terms of widgets performance.
To accomplish the both tasks between the times, you may install both of those perls beforehand, but be careful from their interference, the $PATH environment variable at first and at least: I use Cygwin's perl from Cygwin.BAT shell only.
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