Perl 157 characters
This entry was inspired by gnibbler's Ruby entry, including the part about embedding the cube in the code. Also thanks to Kinopiko for schooling me on the 4 arg version of substr.
@O=($/.$"x99)x99;map{for$n(0..$_-1,$_..-1){map{substr$O[50-2*$n+$_],$W+4/$_,6,
(_,"__"
,"/__ /|",
"| | |",
"|___|/")[$_]}1..4}$W+=4}@ARGV;print grep/\S/,@O
Explanation:
Line 1: Choose where cubes go
Lines 2-5: Put cubes where cubes go, print
