Make sure you put the most common codes at the front of your @codes array for more speed, since you'll do less searching.

Interesting idea... I wonder if dynamically resorting as you go would help?

my @codes = qw/ CODE1 CODE2 CODE3 /;
my %hitCounts;
my @regex = map { $hitCounts{$_}=1; qr/$_/i } @codes;

# tune this parameter for optimal performance, balancing better orderi
+ng
# of regexen with sort costs...
my $resortFreq=1000;

my $iterCount=0;

while (my $inputline = <FILE>) {
    my $found = 0;
    foreach my $regex(@regex) {
        if ($inputline =~ /$regex/) {
            $hitCounts{$regex}++;
            $found = 1;
            last;
        }
    }
    # re-sort every 1000 lines.  The "1000" is a parameter that prolly
+ should
    # be tuned
    if(++$iterCount%$resortFreq == 0) {
        @regex=sort {$hitCounts{$b}<=>$hitCounts{$a}} @regex;
    }
    next unless $found;
    # logic goes here
}
[download]

At the very least, you could do this once, and then feed the results back into the top of the script. If the frequencies are about constant (which makes sense for department populations in a large firm, I guess), this should make a lot more sense than dynamically resorting each time...

END {
   print "Regexen in sorted order:\n\t";
   print join "\n\t",sort {$hitCounts{$b}<=>$hitCounts{$a}} @regex;
   print "\n";
}
[download]

An other alternative would be to have the end block write out a file of regexen, which the script could read back in. Then each run would be as good as it could be, based on the results of the previous run...
--
Mike