I'd recommend dividers—the kind that you can open and close with one hand;
a GPS Plotter
instead of parallel rules or triangles, which moves up and down the chart without moving laterally.
A protractor is a good idea.
Or a Chart Plotter, if you want to have one item that combines the protractor and the parallel rules.
As for pencils... I would highly recommend using a fairly soft lead, like a 2B, as it will leave darker marks on the chart and is softer so will not damage the chart paper as much as harder leads might. A good gum rubber eraser is also highly recommended. If you use a mechanical pencil, go with either .5 or .7 mm lead, anything larger is going to be hard to mark the chart precisely, and anything smaller is hard to see.
A few other things I've found useful.
1) Post-It flags... are good for keeping track of your position on the chart, without having to constantly mark and erase the chart.
2) A mylar or vellum overlay that is large enough to cover the chart can go a long way to helping you mark the chart without damaging it.
3) A large clear plastic envelope or case can serve the same purpose and serve to protect the charts from spray when used in the cockpit.
4) If you use the clear overlays, a grease pencil is a good way to mark the charts for dangers... since it is very, very, obvious.