First of all, you'll want to replace that 'give me a' with a subroutine, since you call it X times. Like so:

sub give_me_a
{
   my ($part_of_speech) = @_;

   print STDOUT "Give me a $part_of_speech: ";
   my $word = <STDIN>;
   chomp($word);
   $word;
}
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More importantly, there're a number of ways you can make the replace more efficient. First, there're a billion text templating modules on CPAN. Text::Template is the most commonly used; that would allow you to do variable substitution directly into the templates, like so:

The quick $adj1 fox ${verb1}ed over the lazy $noun1.
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Better would be to put all of your nouns and adjectives into arrays or hash tables. Something like this would do:

my %word_list = ();

foreach my $part_of_speech ( 'noun', 'verb', 'adj' ) {
   for (my $word_idx = 1; $word_idx <= 3; $word_idx++) {
       $word_list{$part_of_speech}{$word_idx} = give_me_a($part_of_spe
+ech);
   }
}

foreach my $line (@story) {
    $line =~ s/\[(noun|verb|adj)([1-3])\]/$word_list{$1}{$2}/g;
    print STDOUT $line;
}
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I'm not sure at all if that's more elegant, but it's shorter. The completed script is here: "Mad Libs Rewrite" .

stephen