Earlier quoted context omitted.
This isn't very helpful in your specific problem, but typically servers don't have graphical capabilities. So much so, that I was a little baffled when I read that you VNC'ed into one. Instead your local toolchain interacts with the remote. If I wanted to paste something in a file remotely, I'd open it in my local editor (which can ssh into remote machines). If I needed to transfer files back and forth, I'd use an FT…
Are you saying you've found a way to remotely browse the filesystem of your Ubuntu box from within windows (without resorting to FTP?). As in, something that ties into windows explorer and lets you deal with remote files as though they were local? If so, please point me to it. But that's sort of the point I'm trying to make. If the Ubuntu team wants to get Windows devs to try out their thing, they need to make stuff…
I think you're missing the point that admining a Linux server is different. The complete set of tools you need to interact with a remote Linux server is: an SSH client.