Stuff all your data into a hash-of-hashes-of-arrays before printing it:

use warnings;
use strict;

my $line = readline(DATA);
print $line;

my %RepeatNumber;
while (<DATA>) {
    chomp;
    my @obj = split /\|/;
    push @{ $RepeatNumber{ $obj[0] }{app1} }, $obj[2];
    push @{ $RepeatNumber{ $obj[0] }{app2} }, $obj[3];
    $RepeatNumber{ $obj[0] }{name} = $obj[1];
}

for my $n (sort {$a <=> $b} keys %RepeatNumber) {
    my $app1 = join ',', @{ $RepeatNumber{$n}{app1} };
    my $app2 = join ',', @{ $RepeatNumber{$n}{app2} };
    print join('|', $n, $RepeatNumber{$n}{name}, $app1, $app2), "\n";
}

__DATA__
id|Name|app1|app2
1|abc|234|231|
2|xyz|123|215|
1|abc|265|321|
3|asd|213|235|
[download]

Outputs:

id|Name|app1|app2
1|abc|234,265|231,321
2|xyz|123|215
3|asd|213|235
[download]

UPDATED: Use numeric sort (thanks AnomalousMonk)