I generally make notes on the fronts and backs of my printed maps, then transfer those notes (and map if it is still readable) to a binder when I get home. If the map is no longer readable I make a new one and use highlighter to trace my routes, mark my camp(s), or where I found water, what time of year it was, temps, weather, blah blah blah.
I also keep my hunting/scouting reports in the same binder because I want all of that info in one handy place. When I go back to an area already visited I print new map, mark anything I think I might need for that trip,and throw it in the pack.
All of the info is grouped first by area, then by type of game. I make a special point to look for water and mark it.
I have a DeLorme Gazetteer which is huge and I keep that in my truck. I am not particularly happy with this map, but it works. Before heading into an unknown area I take scotch tape and lay it over my intended route. Then I trace the route with highlighter. When I am done with that trip I remove the scotch tape and my map is ready for the next trip.
Loc: California (southern)
I use maps in much the same way, particularly when doing archaeology. In that situation, I am often taking copious field notes (although rarely too copious!) and I usually copy the map to add to the notes and photographs I take. Most of my techniques were developed before field computers, GPS, and digital photography, so i would do things a little differently now. I still often made notes, pinpricks, and the like on the maps, very often using aerial photographs as well.
Nothing is as fundamental and useful as a good map.
Except when the TSA sees your map of Rocky Mountain NP with your marks and then questions you as if you are planning a terrorist attack. If it wouldn't have caused us to miss our flight it might have been funny with the number of people poring over that map with no idea what they were looking at. What is really sad is that none of them appeared to have basic map reading skills.