There is a nice tutorial
on mass-editing of files on perl.com.
The complete list of all the useful command line switches is in the perlrun
What I like to do is combine Perl (to process the files) with the UNIX command line tool "find" (to make the list of files to hand to Perl). If you are on Windows, you can still go with the File::Find module (examples for this are in above tutorial).
Another thing to watch out for if you are writing one-liners with "perl -e" is that you easily run into quoting problems (totally depends on the shell you are using), see Escaping characters in one-liners.