I'm using a DSN of the format:
  mysql://database:password@localhost:/path/to/port/mysql.sock/squirrel

Which seemed like it should work, but it fails because of the way PEAR parses the DSN: Instead of looking for the last / to deliniate the database, it looks for the first. I changed the following lines in DB.php, in the function parseDSN, at line 502:

...
            if (strpos($dsn, '/') !== false) {
                // **THM**
                $offset = strrpos($dsn,'/') ;
                $proto_opts = substr($dsn,0,$offset) ;
                $dsn = substr($dsn,$offset+1);

             //  old: list($proto_opts, $dsn) = explode('/', $dsn, 2);
            } else {

...

This fixes the problem and should remain compatible with numeric ports as well. A quick scan of the web site didn't reveal how to submit patches, so I hope this is Kosher.