why use two passes? Give GetOptions a sub to call instead.

use Getopt::Long;
my (@foos, @bars, @bazen, @quuxi);
GetOptions (
    'foos=s'  => sub { shift; push @foos, split /,/, @_; },
    'bars=s'  => sub { shift; push @bars, split /,/, @_; },
    'bazen=s' => sub { shift; push @bazen, split /,/, @_; },
    'quuxi=s' => sub { shift; push @quuxi, split /,/, @_; },
);
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of course, since your option names exactly match your arrays, something like this should work...

use Getopt::Long;
my (@foos, @bars, @bazen, @quuxi);
sub setter {
   no strict refs;
   push @{shift}, split /,/, @_;
}
GetOptions (
    'foos=s'  => \setter,
    'bars=s'  => \setter,
    'bazen=s' => \setter,
    'quuxi=s' => \setter,
);
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but at that point you should just use...

use Getopt::Long;
my %opts;
sub setter {
   push @{$opts{shift}}, split /,/, @_;  
}
GetOptions (
    'foos=s'  => \setter,
    'bars=s'  => \setter,
    'bazen=s' => \setter,
    'quuxi=s' => \setter,
);
[download]

(All of that is completely untested ... I'm sure I have some syntax typos).

Update: Yeah, What Roy said....