I use openssh server in my ubuntu desktop to connect from my phone. ES File Explorer can connect by ssh to my desktop and I can transfer files easily. To do more advanced control from my desktop I also use QtADB http://qtadb.wordpress.com/
QtADB supposedly also works on Windows. But you could also you an ftp or ssh server on the phone and an ftp/ssh client on Windows (e.g. FileZilla or WinSCP). And there's File Expert that allows sharing via HTTP (browser) or FTP.