PHP - 447 398
I Know it's not as short as the others here, but I'm happy with it ;)
$g=$argv;unset($g[0]);$c=array('|___|/',' '=>'| | |','/__
/|',3=>'__');$x=max(max($g),0);$m=$i=min(min($g),0);$row=$y=0;
while($x>=$i){$n=$row++*2;foreach ($c as $w=>$p){
$L[]=str_pad('',count($g)*4," ");$t='';$y=0;foreach ($g as $h)
{if((($h>=$i&&$i>0)||($h<$i&&$i<=0)))$L[$n]=substr_replace($L[$n],$p,4*$y+$w,
strlen($p));$y++;}$n++;}$i++;}array_splice($L,$n);krsort($L);
print implode("\n",$L);?>
Input / Output
C:\development\code-golf>php cubes1.php 1 2 1 -5 -5 4 3 3
__
/__ /|
| | |__ __
|___|/__ /__ /|
__ | | | | |
/__ /| |___|___|___|/|
_| | |__ | | | | |
/__|___|/__ /| |___|___|___|/|
| | | | |__ _| | | | |
|___|___|___|/__ /__|___|___|___|/
| | | |
|___|___|/|
| | | |
|___|___|/|
| | | |
|___|___|/|
| | | |
|___|___|/|
| | | |
|___|___|/