I'd approach this by splitting the package names into a hash, and then comparing those:

#!/usr/local/bin/perl -w
use strict;
my %installed;
my %updates;
# __DATA__ juggling below is just a kludge to simulate list files
while (<DATA>) {
  my $target=$.>5?\%updates:\%installed;
  # Regex works on your limited sample, but is quite weak.
  /(.*?)-(\d.*)/;
  $target->{$1}=$2;
}
foreach my $package (keys %updates) {
  delete $updates{$package} unless (exists $installed{$package} && ($i
+nstalled{$package} ne $updates{$package}));
}
print "Packages to update:";
print join "-", ($_,$updates{$_}), print "\n" for keys %updates;
__DATA__
zip-2.3.1-14
xpdf-1.01-8
ggv-1.99.8-2
libpng-devel-1.2.2-8
xvattr-1.3-ogle1
WindowMaker-0.80.1-5
lynx-2.8.5-7.1
xpdf-1.01-10
ggv-1.99.9-5
xvattr-1.4-ogle1
libpng-devel-1.2.2-9
__END__
Packages to update:
ggv-1.99.9-5-1
xvattr-1.4-ogle1-1
xpdf-1.01-10-1
libpng-devel-1.2.2-9-1
[download]

However, the crux of your problem, comparing version numbers, is not dealt with by this - it just spits out the package if it has a different version, not necessarily a higher one. And, as stated in the code, the regex I use is probably easily defeated by some of the more exotic version names (it just splits on the first dash which is followed by a number).

However, this should give you some idea on how to procede.

CU
Robartes-