Just to be different, I prefer the Jeppesen paper charts, so for permanent marking I use biro, and for temporary marking, soft pencil.
As to what, it depends upon what I'm flying. If I'm in a light (or occasionally not so light) aircraft that allows me to have a guide next to me, it'll have little more than track lines, headings, and segment distances.
If I'm flying a microlight, I'll include approach details, times, magnetic corrections - basically everything since you really need everything on your map in an open cockpit. To a lesser extent, I do the same in an enclosed single seater - although you can at-least put your approach plate separately.
One reason I switched to Jeppesens, is that when I last used one, the CAA chart didn't include radio frequencies, morse idents and runway lengths and directions, which Jeppesens does (and I used to add in with fine OHP pens to my CAA chart). If the CAA charts have changed since then, the Jeps are still cheaper and fit in my kneeboard more easily.
G