Predeclaring arrays isn't generally necessary -- there's a bit of a performance benefit as dynamic memory allocation isn't necessary, but Perl handles that sanely anyway.

Caveats aside, save a few characters: my @x = ( 0 ) x 25;

This construct could also be more concise:

while(defined(my $line = <FILE>)) {
    next if ($line =~ /#.*?,/);
    my @units=split(/,/, $line);
    for ($i = 0; $i <= 23; $i++)
    {
        if ($line =~ /$xcounits[$i]/)
        {
                   $y[$i]++;
            $ytot++; 
            $x[$i] += $units[5];
            $xtot += $units[5];
        }
    }
}
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The defined is in there just in case. (I believe the magic <FH> read does this for you, but I don't have time to look up to make sure assigning to a variable explicitly does.)

The regex could be less cautious. If you want to skip comments, it's a lot easier just to do next if $line =~ /^#/;.

The loop there makes me wonder if you're better off with a hash. Anytime you find yourself looping through an array, looking for a particular element, you should ask if a hash would be more appropriate.

Looks like your next hurdle is learning some Perl idioms to make your life easier. Don't worry, they make more sense once you use them a few times.

Update: moen is right, so I fixed that little issue. Thanks!