A.6.7 How do I use all PuTTY's features (public keys, proxying, cipher selection, etc.) in PSCP, PSFTP and Plink?
Most major features (e.g., public keys, port forwarding) are available through command line options. See the documentation.
Not all features are accessible from the command line yet, although we'd like to fix this. In the meantime, you can use most of PuTTY's features if you create a PuTTY saved session, and then use the name of the saved session on the command line in place of a hostname. This works for PSCP, PSFTP and Plink (but don't expect port forwarding in the file transfer applications!).