Let me add that as you progress through Learning Perl (and then Intermediate Perl), what is taught will start to converge with Modern Perl principles reasonably well.
As chromatic said, Learning Perl is designed to teach programming as well as Perl, so it focuses on one thing at a time and ignores some good practices early on to avoid confusion.
I recommend the latest edition of Intermediate Perl after Learning Perl and then Effective Perl Programming and/or Modern Perl after that.
Stay away from Higher Order Perl until you consider yourself a "pretty good" programmer — or if you really enjoy the theoretical aspects of programming. It's a great book, but probably more confusing than helpful in the early years.
I'm not a fan of Mastering Perl or Advanced Perl Programming. They have some useful bits, but nothing critical. Possibly the rewrite of Mastering Perl (not yet published) will improve it.
I loved the Perl Cookbook years ago, but it's rather out of date now. It might be useful for recipes to get things done, but I wouldn't look to it as a guide for good ways to do things. You'll probably get better answers asking here.
Avoid Object Oriented Perl. Horribly outdated.
Perl Best Practices is good but needs to be taken with many grains of salt. There are good things there, but there are very opinionated/bad things there. I think there are discussions somewhere on this site about it. Save it for later when you start to have your own opinions about good ways to do things for context and don't use it as gospel.
Hope that helps guide you.
(N.B: I was a technical reviewer for Intermediate Perl)
-xdg
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