... was asked for pointers in a private mail; here is my quick and dirty answer:
I am no shell expert (have read and modified lots of scripts, but have not written any advanced stuff from scratch); for BASH I recommend http://tldp.org/HOWTO/Bash-Prog-Intro-HOWTO.html;
for Perl: the documentation packaged as man pages is very good (do a "man perl" to get the index), and in book form almost anything from O'Reilly is good (they are the unofficial sponsors of Perl ;) ) , this one is a must http://oreilly.com/catalog/9780596000271 , this one is a good place to start http://oreilly.com/catalog/9780596520113 , and http://www.onyxneon.com/books/modern_perl/index.html as soon as you're done with "Learning Perl" .
Anything signed by Randal Schwartz, Damian Conway, chromatic, Larry Wall, Tom Christiansen (and others, but those are the names I remember now) is worth reading, whether in print or on the web.
you can find books online here http://www.perl.org/learn.html , and some other links here http://oreilly.com/perl/
If you're on windows get Active Perl http://www.activestate.com/activeperl or Strawberry Perl http://strawberryperl.com/ , both are very good. Indigo Perl used to be in vogue years ago, might not be a bad choice http://www.indigostar.com/indigoperl.php ... a long time ago I used to use Indigo Perl when exiled in M.S. land, so I am a bit partial to them :), but Strawberry Perl appears to be the "official" Windows port of Perl.
If you know Unix/Linux reasonably well, you could try http://www.cygwin.com/ : you get a lot of unix tools running on windows including perl, or install Linux in a virtual machine (I recommend VirtualBox, but Parallels and VMWare make good tools, too).