It is not particularly short, but the following 133 solution at least looks to be a valid solution to the problem: 
sub f{
#23456789_123456789_123456789_123456789_123456789_123456789_123456789_
+123456789_123456789_123456789_123456789_123456789_123456789_123
%h=@_;$h{$_}||=[]for map@$_,values%h;for(@k=keys%h){for$x(@k){push@{$h
+{$x}},@{$h{$_}}for@{$h{$x}}}}sort{-1+2*grep$_ eq$b,@{$h{$a}}}@k
}

[download]
The thing that I do differently than previous solutions is add a step where I follow dependencies. Since the longest chain of dependencies is cannot be longer than the number of elements, I just need to repeat that step the right number of times.

In reply to Re (tilly) 1: (Golf) Dependency List Prioritization by tilly
in thread (Golf) Dependency List Prioritization by tadman

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