Matt, you hit the nail on the head with avoiding notes by using clever names. That was how I did it in the Terramodel days, when 16 characters was the limit it was very challenging. Now with TBC having much longer layer names it is somewhat simpler. However I still find myself maintaining a spreadsheet of layers and surfaces with notes about them. For example: suppose I made a finish grade surface for Ramp A and I name the surface and the layer that contains the surface linework "Ramp A - FG". Then for any number of various reasons there is a revision to the curb location, so I make a copy of the surface, change the name to "Ramp A - FG R1" and make the changes to the curb. Then another change comes along for the cross slope of the ramp, so then I go to "Ramp A - FG R2" and then another and another and another. Its not uncommon for me to have 10 revisions to a surface before it is complete. I've even had nearly 100 revisions to a surface. And invariably for example at some point the owner will say after 6 revisions have been made, oh lets not do that curb revision and go back to the original curb location. Then I have to pull out my notebook to go back through my notes about each revision number to see where the curb change took place.
And this is just one of very many instances where I need notes about what I have done. I also frequently design waste piles, and borrow pits. They will be very many changes to the design, and I will need to know exactly what changes were made with each revision so I can go back to a previous state, or also so I can compute changes in quantities between certain revisions.
Additionally I find myself creating multiple corridors of the same alignment for testing various things out, and it would be very helpful to have a notes section for not only the corridor itself, but also for each template on the corridor. I typically model finish grade, subgrade, and every material layer in a corridor which amounts to several dozen instructions. It would be very helpful to have a note section so I can remember why I had to put that particular template in there because it is not always obvious and can be very cumbersome to try to describe in the name.
As far as the best way to keep it from being cluttered as you mentioned, I think if the note was just a property that is shown at the bottom of the list on any entity's properties it would really not add any clutter.