I suppose I would start with simply searching the code for the subroutine names, but what if you had any of the following:

#1
print "Enter some Perl code: ";
eval ($this_is_a_great_design = <STDIN>);

#2
my $result = &{ $control_db->{"action"} };

#3
my @foo_functions = map (\&("foo_".$_)) @bar;
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Well, the first one is ridiculous in a CGI script, but what about the others? Well, I guess you could turn on

use strict qw/refs/;
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and if this didn't break the existing code, I think you would be guaranteed to find the name of every sub that is used in the code somewhere.