my %exeDll;
for ( @exeDllLines )
{
        chomp;
        my @a = grep /\S/, split /,/; # split on comma; filter out empty fields
        my @dlls = grep /\.dll$/, @a; # get list of dll files
        for my $exe ( grep /\.exe$/, @a )
        {
                @{$exeDll{$exe}}{@dlls} = ()
                # OR:
                $exeDll{$exe}{$_}++ for @dlls;
        }
}

# then you can iterate over the collected data:

for my $exe ( sort keys %exeDll )
{
    print "$exe uses the following DLLs:\n";
    for my $dll ( sort keys %{ $exeDll{$exe} } )
    {
        print "\t$dll\n";
    }
}