While there might be some good reasons to use the Unix toolkit I've seen people shell out for the simple reason that they had not taken the time to figure out you can do it in Perl.
I've pointed out to a cowoker that you really don't need to do this...
my @files = `ls *`;
...when this would suffice:
my @files = <*>;
I've also seen the following crop up from time to time:
my $now = `date`;
system("rm testfile");
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