Here's another version. I was about to post it, but then I saw CountZero's solution above, which uses pretty much the same procedure. However, as mine looks more concise, I thought, why not? FWIW:

my $elem = 1;
my $k = 3;
my %out;

while ( <DATA> ) {
   next unless /\b$elem\b/;
   $out{$_}++ for split;
}

delete $out{$elem};
print "$_ ($out{$_} times)\n" for 
   (sort { $out{$b} <=> $out{$a} } keys %out)[ 0 .. ( $k - 1 ) ];
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dave