This is for version 4.44 of the Pine client. It should be basically the same for any recent version.
"POPFILE" {127.0.0.1/pop3/user=<user>_<host>}INBOX
That should be it. As you train POPFile, Pine will filter your mail whenever you open the POPFILE folder.
Note: For those folders that you want to filter to but you don't want to navigate through by default (I have 'spam' and 'virus'), create the folder, but don't add it to Incoming folders. If you already have, you can edit the list in your pinerc file. This lets you tab through the folders you actually want to read, and go to the bad folders through the Local Folders interface.
Should you find anything in the documentation that is incomplete, unclear, outdated or just plain wrong, please let us know and leave a note in the Documentation Forum.