The simple approach is to draw the elements from back to front.

The hard part is to find out which element is in the back and which is in the front, the "z-order" of the elements.

Let's assume for a second i knew which object are in the back, even then, how do i need to draw this? I've added my code.

use GD;
use constant PI    => 4 * atan2(1, 1);
$im = new GD::Image(400,400);
$black = $im->colorAllocate(0,0,0);
$red=$im->colorAllocate(255,0,0);
$green=$im->colorAllocate(0,255,0);
$im->filledEllipse(200,200,50,50,$red);
$im->filledEllipse(300,200,25,25,$green);
for($xy=0;$xy<6.28;$xy+=0.01){
$x = 100*cos($xy);
$y = (43.75/2)*sin($xy);
push @punten,[200+$x,200+$y];
    }
$data =$im->gifanimbegin(1,0);
$data.=$im->gifanimadd(1,0,0,1);
    
for($z=0;$z<=$#punten;$z+=20){
$ima = new GD::Image(400,400);
$black = $ima->colorAllocate(0,0,0);
$red=$ima->colorAllocate(255,0,0);
$green=$ima->colorAllocate(0,255,0);
$ima->filledEllipse(200,200,50,50,$red);
$xc = $punten[$z][0];
$yc = $punten[$z][1];
$ima->filledEllipse($xc,$yc,25,25,$green);
$data.=    $ima->gifanimadd(1,0,0,1);
    }    
$data.=$ima->gifanimend;
binmode STDOUT;
print $data;
[download]

Instead of drawing $red and then drawing $green, you need to find out which of the two is in the back, and draw that one first.

For example, do it like this:

# Define the two planets
my @large= ($red,   200,200,50,50 );
my @small= ($green, $xc, $yc, 25, 25 );

my( $front, $back );

if( $red_is_in_front_of_green ) {
    $front= \@large;
    $back= \@small;
} else {
    $front= \@small;
    $back= \@large;
};

# Just in case we ever go beyond two objects
my @objects_to_draw= ($back, $front);

for my $item (@objects_to_draw) {
    my( $color, @position )= @$item;
    $ima->filledEllipse( @position, $color );
};
[download]

• The position in space (and orientation) of the camera, and the dimensions of its viewport.
• The position-in-space of the sun, the center of orbit.
• The distance and angle (polar coordinates) of each planet, which may be converted to absolute (x,y,z).