On mouseover, mark the node you're hovering over, and color its neighbours according to the type of the relationship. This style is only an example and anything goes - from adding icons, respecting asymmetric links (i.e. different markup of employee or manager in an unmutual hierarchy link) and the list goes on.
Not relying on markers etc gives a lot of visual relief.
Based on Mike Bostock's molecule example from: http://bl.ocks.org/mbostock/3037015