Setting unicode, changing backspace, setting xterm-256 as the TERM variable, etc ... PuTTy configuration is unintuitive when you first try to configure it. There's a well known page dedicated to configuring PuTTy properly on Windows.
I haven't tested this extensively myself, but have you looked at ExtraPuTTY?
http://www.extraputty.com/features.html
Seems like one of its goals is to make it easier to move PuTTY configurations from one machine to another.
What sorts of configs have you had to do for Putty?