I have been making a few small tweaks to my host software to improve quality recently. One such tweak is the order in which islands of an object (or objects) are visited. By "island" I mean a closed outline and the holes and infill that it encloses. Skeinforge seems to always go for the nearest island, so when it finishes a layer it starts the next layer on the island it has just done and revisits the others in the reverse order.
This means that the plastic is added to the hottest island first and the coldest last. When an island is small it can mean that the layer below is still molten when the next layer is added. I simply reverse the order of every second layer so that the islands are visited in a round robin order. That means they all get the same time to cool down before the next layer is added.
The only downside is one extra long head move each layer from the last to the first island. If your machine leaves strings that is not ideal but mine hasn't since I started reversing the extruder. That also makes the Comb and Tower modules of Skeinforge redundant.