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.