I've always just used Term::Shell - it seems to be used a lot, but after a little extra searching, I think maybe I prefer Term::ShellUI, which is newer and more flexible.
Here's another argument for some kind of curation or functional grouping of CPAN.
Incidentally, looking for shell modules, I also ran across Net::CLI::Interact, used for talking to shells over the network.
Update 2012-10-02: Yep, Term::ShellUI is a pure joy to work with. (I started Shell::SQP based on it yesterday, with entirely satisfactory results.)
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