Public key authentication in PuTTY uses SSH keys stored in .ppk files. Instructions for configuring public key authentiation for PuTTY can be found here.
There have been documented instances of malware collecting PuTTY SSH keys. In the widely publicized Sony breach, attackers went after .ppk files. This illustrates how important SSH key management is. As of this writing, Universal SSH Key Manager is the only SSH key management solution that supports PuTTY keys.
