i mentioned this in Map Making Help as you can easily create your own physics sim for the parts eg.
force (0,-1,0)
force for each other object relative to direction (0,0,-(mysize+othersize)/d) (rounded down if below 1 or similar)
attractive force to connected bodies relative to direction (0,0,(d-(connectionlength))/strength)
random force (±0.01,±0.01,±0.01) (stops things stacking up)
Then just draw some lines and do a projection if you want it in 3d.