I have used the colour to distinguish individual families (ie those with the same surname) - on a large tree I find this helps identification. I use the size/thickness to identify the closeness of relationship to a specific individual or family on the tree - the more distant the relationship the smaller/thinner the label/line. This is perhaps not something to do regularly with a large tree, but it can enhance a more restricted tree for presentation purposes.
The introduction of GenopMaps has to some extent negated the use of these techniques, but I still find them useful, especially for printed family trees.