I had been thinking that all visible options would just be in an "options" item on the main menu -- whether they be noteye, or the adom.cfg, laid out by category. (Possibly with sub-menu's for some of it.) For example (a random selection .. you might prefer some of them to be invisible):
Sound
Music Volume
Sound Volume
Graphics
Inventory Graphics on/off
Show Animation
Show Blood
Tile Size
Gameplay
Automatically Open Doors
Automatically Pick-up These Items (when auto-pickup is turned on):
amulets, arrows, scrolls, gold, books, rings
No Book Spellcasting
Mouse control
Auto-Centering Speed ---------|- (that's a slider) :)
Manual scrolling region -----|------
Manual scrolling speed -|----------
Scroll-Wheel on/off
Information
Coloured Messages
Show Experience
Show Healthbars
Misc
Exit ADOM after player death
Exit ADOM after saving the game
The real challenge, I guess, is what to make invisible. :) ..and, of course, the invisible ones can still be changed in the relevant cfg file.
(I'm just throwing around ideas, of course. ..feel free to use all of it, or none of it.) :)