You are heading in the right direction. If you wrap the essence of your code in a for loop that iterates over the files you need to process and change the hash access from an assignment to a += then you've done the input part. Generating the output is then a matter of two nested loops. Consider:

use strict;
use warnings;

my $file1 = <<END_FILE1;
0: 0,11 5,6 11,2
1: 1,3
3: 0,1 2,2 3,2
5: 3,5 6,1 8,16 9,1
END_FILE1

my $file2 = <<END_FILE2;
0: 0,10 4,19
2: 1,3 2,5 6,4
5: 6,10 9,3
END_FILE2

my %sites;

for my $source (\$file1, \$file2) {
    open my $inFile, '<', $source or die "Failed to open $source: $!\n
+";

    while (my $line = <$inFile>) {
        chomp $line;
        
        next if ! ($line =~ s/^([^:]+):\s*//);

        my $word = $1;

        for my $field (split ' ', $line) {
            my ($site, $count) = split /,/, $field;

            $sites{$word}{$site} += $count;
        }
    }
}


for my $word (sort {$a <=> $b} keys %sites) {
    print "$word: ";
    
    my $wordSites = $sites{$word};
    
    for my $site (sort {$a <=> $b} keys %$wordSites) {
        print "$site,$wordSites->{$site} ";
    }
    
    print "\n";
}
[download]

Prints:

0: 0,21 4,19 5,6 11,2 
1: 1,3 
2: 1,3 2,5 6,4 
3: 0,1 2,2 3,2 
5: 3,5 6,11 8,16 9,4
[download]

There are a few things you ought do to save yourself time in the future. First off, always use strictures (use strict; use warnings;). Use the three parameter version of open (you didn't did you?) and always test the result of file opens. Use lexical file handles (open my $infile ...).

Note the indentation and bracketing style I've used in my sample. It is pretty common in Perl circles and is probably worth adopting. There is a really good tool called Perl Tidy that is well worth getting if you are at all interested in generating consistently formatted code.