Hi, Jim.
The # of hops is the number of routers between you and the target. This is relatively fixed in most situations (there are only so many routers between you and the target you're targetting with PingPlotter).
The number of samples refers to the number of times PingPlotter collects data from that target. If you have a trace interval set to 5 seconds, then you're going to get one new sample set every 5 seconds.
The "Samples to include" setting refers to the number of samples you're examining in the graph (which also gets brought over to the export feature as default starting and ending ranges for the export).
We cover most of this in our getting started guide (
http://www.pingplotter.com/gsg). Please let us know if this leaves you with questions, or if I misunderstood your question.