There are versions of PuTTY that store the config in files, usually with names like Porta-PuTTY. I use the hacked up Xming Portable Putty because I do a lot of X forwarding and the base PuTTY used to have some stability issues with it. They're probably fixed now, but I still use the hacked up PuTTY because my configs are in the text files instead of the Registry and regular PuTTY doesn't know about them.