"Click on graphical directory tree view to send a 'cd /clicked/directory' to the command line of PuTTY (and execute it)."
Ok, so my personal biggest complaint with using any kind of command line is changing directories... there is a lot of typing involved to get where you want to be, and generally there are quite a few spelling mistakes along the way that end up not taking you where you want to go, but instead you need to re-type the entire command again. I am of course talking about the "cd - change directory" command!
Specifically I am talking about using PuTTY as my terminal/console to access my Linux server over ssh, but this issue goes all the way back to the Windows DOS days as well, and is a problem with any command line interface... there is just no easy to change/navigate directories! The problem also exists when using the WinSCP terminal/console as well... if you want to change directory, you still need to to type "cd bla/bla/bla".
My suggestion is to have some kind of graphical directory tree that would appear in it's own window and could be (for example) docked to the right side of the PuTTY terminal/console command line screen. It would have +expand/-collapse icons for each directory, and clicking on a specific directory would cause a "cd /directory/that/I/clicked/on" command to be executed in PuTTY. What I mean by 'graphical directory tree', is something similar to the Remote File View you see in the main WinSCP window, except it would be striped down... it would ONLY show the Name column, it would ONLY show directory names (no files), and it would not show any buttons/menus of any kind.
It would be accessed by adding a new option under COMMANDS called "Open in PuTTY with Directory Tree". Clicking this option would start a PuTTY session just like normal, but would also popup the directory tree view that could be clicked on to execute the change directory command, instead of having to type cd.
Possible sources of information that may help:
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Hope this a feature worth consideration.