Well, if you can guarantee that LIST 2's packages will always be later than LIST 1's, you might be able to do this:

#
# build some lists for testing purposes...
#
my @current = qw (
zip-2.3.1-14
xpdf-1.01-8
ggv-1.99.8-2
libpng-devel-1.2.2-8
xvattr-1.3-ogle1
);

my @updates = qw (
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
);

#
#  Ok, here's the real code snippet.
#
my %one;
my %two;

foreach ( @current, @updates )
{
   if (/^(\w+)-/)
   {
      $two{$_}++ if $one{$1};
      $one{$1}++;
   }
}

print join( "\n", sort keys %two );
[download]

Output:

C:\Perl\bin>perl upgrade.pl
ggv-1.99.9-5
libpng-devel-1.2.2-9
xpdf-1.01-10
xvattr-1.4-ogle1

Rob