Prior to scouting trips I use GE to create a game plan of areas I think have potential. I drop pins, record the coordinates and enter the waypoints one by one while in the woods. I do this because no matter how much time you spend looking at aerial imagery things appear sooo much different with boots on the ground and I rarely end up at the point I thought was so prime from my computer screen. As far as naming waypoints I tend to use unique names from the first time I found that area. For instance I have places named airplane ridge (for the plane wreckage there), the grizz hole (from a memorable chew of grizz mint I had) and my favorite… the glory hole (for a couple satellites we called in at full mast). I tried the generic honey holes and elk creek rub names and found they all ran together after multiple years of hunting the same area. Probably not as systematic as you were thinking but has worked for me.
I think any method that works for ya is a good one. Im guessing my final method will be a combination of a systematic file structure, and a few of those "special names" that you just discussed. I can remember certain details of every hunt, and those special places will probably get the types of names you have discussed above.
I have this problem with overanalyzing things sometimes, but what Im thinking is that as Im walking around on a hunt or scout, Id like something quick and easy....so lets use this example. I go to hunt a new area in Wy, and I park the truck. First waypoint is 001 truck. Then I walk up the mountain, and see a wallow, so that becomes 002 Wal. Then I come to a southern facing ridgeline and find an elk shed, that would be 003 Eshed. Im thinking a three or four letter code for each type of waypoint would minimize the on screen clutter on the GPS too, and maybe help put pieces of the puzzle together while on the hunt.
When the hunt is over, I have a list of waypoints numbered, but also have a brief method of naming each waypoint for future use as a scouting tool. Im not sure how many characters Ill have to work with, but im guessing 10 from what I read for the garmin units. From there, its back to Garmin basecamp to put them in a folder specific to that area. Because there is only a certain amount of waypoints available for storage, if we are marking all of these things we see during a hunt or scout, Im guessing a guy could run out of waypoints after a season of hunting pretty easily.
So keep the info coming. Im doing some tutorial videos on the Garmin basecamp trying to figure that out too. I thought Id be able to use google earth and work directly from the GPS, but from what im reading...ill have to use the garmin base camp as the go between.
lets hear your systems to stay organized with waypoints, scouts, hunts, etc for later viewing and use.