Since starting to use Windows 8, I found that the grouping behavior of the taskbar combined with a dozen open PuTTY windows drove me insane. There's a multiple-tabbed PuTTY shell, but it was hard to get used to as well. I finally switched to the Chrome SSH client, which has been much better (though it doesn't have nearly the features of PuTTY, of course).
It's been a while since I was stuck on a Windows box, but I found the combination of Console2 (tabbed terminal emulator) with Cygwin[1] was quite nice. Then you can use `ssh', `scp', etc. like you would on a Unix machine. You might want to try this approach if you're willing to go as far as to do this from your browser (which gives me shivers). This was on Windows XP but I imagine it still works. [1] http://sourcefor…
I played with "Putty Session Manager" for a while before moving entirely to Mintty under Cygwin.