How do other sch handle all the keybinds?

My current Scholar keybinds look like this:
http://i.imgur.com/XTSNjfx.jpg

The small row of icons under the 1-4 range is bound to Alt+1-4, and the one under my summon buttons is Ctrl+1-4.
The 'numpad' block is mapped to the thumb buttons on my G600 mouse, and I use the 'mouse shift' button to also be able to hit the Insert->Page Down range of buttons, along with Ctrl+1-3.

My overall advice is to make liberal use of alt and ctrl, as well as use easily accessible letters as keybinds as well. I discussed this with a friend the other day, and he uses Z/X/C along with shift/alt/ctrl variations, if I didn't have a fancy mouse, I'd likely have things bound to R/F/T, with autorun and focus target (Edit: and target target's target! Dunno how I forgot that one when I use it all the time.) moved to the bottom row of letters.

I've played with a naga for years. I can comfortably hit 48 key binds alone with modifiers shift, ctrl, and alt.

Ctrl and shift are really easy on most keyboards. Alt might be a bit tougher depending on your keyboard and your dexterity. So as others have suggested you can bind things around your movement keys which you can double/triple up on with modifier keys as well. I did this prior to having a naga.