WinSCP and Puttyt are small but convenient IT tools. Unfortunately they lack backup tools, so moving yourconfiguration to a different machine or restoring after reinstallation seems like a problem. But it is really not a problem if you are familiar with Windows registry.
Putty
HKEY_CURRENT_USER\Software\SimonTatham (export the key and merge it later)
WinSCP
HKEY_CURRENT_USER\Software\Martin Prikryl (export the key and merge it later)