If one writes java code in Perl one should not be surprised of the bad performance.

The following is a more perlish version:

use Modern::Perl;
use Time::HiRes qw/time/;

my $start = time;
my $top   = 550;
my $max   = 100;
my @primes;
my $prime;

for ( 2 .. $top ) {
    $prime = $_;
    next if $primes[$_];
    last unless --$max;
    {
        local $_;
        $primes[ $_ * $prime ] = 1 for 2 .. $top / $prime;
    }
}
my $found = time;
say $_ for ( grep { !$primes[$_] } 2 .. $prime );

my $end = time;
say sprintf "Found all:    %.6f seconds", ( $found - $start );
say sprintf "Printing all: %.6f seconds", ( $end - $found );
say sprintf "Running time: %.6f seconds", ( $end - $start );
[download]

Output:

2
3
5
7
11
13
17
19
23
29
31
...
491
499
503
509
521
523
541
Found all:    0.000692 seconds
Printing all: 0.000879 seconds
Running time: 0.001571 seconds
[download]

This application of the Sieve of Erasthotenes finds 100_000 primes in 3 seconds (and then takes 6 seconds to print them on the screen), so it is pretty fast.