I have a couple of *nix machines I transfer files to/from. I currently don't have a need to do this in a completely automated way (may in the future).

I use the FireFTP plugin to Firefox browser for file transfer and putty for command line stuff (like run the program when it gets to the server/other machine).

FireFTP gets you a graphical "drag and drop" interface that is pretty smart. You can also sync directories and directories + sub-directories. And some other fancy stuff that I haven't needed yet.

Anyway, I just click on FireFTP, click on connect to server and then move stuff around and rename, etc. in a similar way to the Windows graphical interface. I find this combination of graphical file transfer window and command line putty window to be fine.

Update: I keep both windows open at the same time. Also, I can open a file on the remote *nix machine in one of my local Windows editors without "moving the file" manually. I just right click and use "Open With..." menu. So I can edit say a Word .doc file on the server without having to explicitly download it, edit it and move it back. When I "save the file", the WinWord changes get updated on the server. For something like that, this looks very much like a local file. If this is what you need to do, I highly recommend it.