Recently I’ve noticed a few examples where smallish visual design details really matter.
What Colin Ware in “Visual Thinking for Design” refers to as “multiscale structure” in shown-off very effectively in Vizster and SocialAction.
Another example is the way that Thinkbase constructs links of similar types: 
Notice how the actors & roles aren’t linked directly to the film but go via intermediate nodes. And also see how well the space is used and how the links are similar lengths & short – both of these are great for aesthetics and link-following tasks.
Both these approaches build on the position visual variable to effectively to ‘clump’ the like-nodes together. But these designs also add other visual variables (connecting line, enclosing shape) which assist visual pattern finding, and importantly can offer affordances for interactivity too.
about the third graph :
it goes beyond the visualization thing, but is also about data model : ie how do you model a phone call ? Alice linked to Bob, with the link containing timestamp, etc ? Or Alice linked to her phone linked to a unique call (witth timestamp, etc), linked to Bob phone, linked to Bob (ok ?), and the phones and call also linked to the cell site coordinates, etc ? which info do you forget, which one do you isolate on your graph ?