#!/perl -l
use strict;
use warnings;

my %merge;

while ( <DATA> )
{
    chomp;
    my ($key, $value) = split /\t/;
    $merge{$key}{$value} = $value;
}

for my $key ( keys %merge )
{
    my @values = keys %{$merge{$key}};
    print "$key => @values";
}

__DATA__
1   101
2   102
3   103
1   104
2   102
3   104


__output__
1 => 104 101
3 => 104 103
2 => 102
[download]

Update: First draft was wrong, misread of the question. Updated within 2 minutes. Apologies if anyone read the first version. :)

#!/usr/bin/perl
my %t;
while ( defined($_ = <DATA>) ){
  chomp;
  my ($k, $v) = split /\s+/;
  push @{$t{$k}}, $v;
}
for ( sort keys %t ) {
  my %q;
  @q{@{$t{$_}}} = ();
  print "$_ ", join( ' ', sort keys %q), "\n";
}
__DATA__
1    101
2    102
3    103
1    104
2    102
3    104
[download]

my %unique;
while ( my $line = <DATA> ) {
    chomp $line;
    my ( $left, $right ) = split /\s+/, $line;
    push @{$unique{$left}}, $right;
}
foreach my $key ( sort keys %unique ) {
    print "$_\t";
    foreach my $item ( @{$unique{$key}} ) {
        print "$item ";
    }
    print "\n";
}
[download]

You made the same mistake that I did at first. The OP wants to not only merge the values by keys, but also remove duplicate values for each key...

--
edan