Update: Just to clarify, the answer I give below assumes that you're interested in a general solution, not just the case where "213119_at" is the only value of interest, as other posts seem to assume from the literal sample you gave. I base this on the comment at the end of your post:

"I would then choose ENSG00000123643 to store in another hash with 213119_at, e.g. 213119_at{ENSG00000123643}.

Storing it in a hash makes me think that you're wanting to do this for all other similar values as well.

Original:

While, I'm sure this could be golfed, my thought is just to build it up in the stages you describe. (Note, I changed some numbers to get two answers in the final hash.) 

use strict;
use warnings;
use Data::Dump::Streamer;

my %original = split " ", do { local $/; <DATA> };

my %count;

while ( my( $k, $v ) = each %original ) {
    $k =~ s/\A[^:]+:[^:]+:([^:]+).*/$1/;
    $count{$k}{$v}++;
}

my %summary;

while ( my ($k, $v ) = each %count ) {
    my $max = [ sort { $v->{$b} <=> $v->{$a} } keys %$v]->[0];
    $summary{$k} = $max;
}

Dump \%summary;

__DATA__
Affy:HG_U133A:213119_at:74:303;         ENSG00000123643
Affy:HG_U133A:213119_at:542:439;        ENSG00000123643
Affy:HG_U133A:213119_at:658:369;        ENSG00000123643
Affy:HG_U133A:213119_at:199:255;        ENSG00000123643
Affy:HG_U133A:213119_at:436:453;        ENSG00000123643
Affy:HG_U133A:213119_at:324:381;        ENSG00000458158
Affy:HG_U133A:213118_at:584:557;        ENSG00000123623
Affy:HG_U133A:213118_at:234:507;        ENSG00000123623
Affy:HG_U133A:213118_at:482:429;        ENSG00000123623
Affy:HG_U133A:213118_at:608:451;        ENSG00000458158
Affy:HG_U133A:213118_at:356:297;        ENSG00000123623

[download]

Prints

$HASH1 = {
           "213118_at" => 'ENSG00000123623',
           "213119_at" => 'ENSG00000123643'
         };

[download]

-xdg

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In reply to Re: Counting hash values by xdg
in thread Counting hash values by MonkPaul

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