I'd start with the obvious ones like basic views, weapons, roll and pitch on the stick, yaw and throttle on the throttle.
On my T16000m stick I also have the Zoom and Clipboard toggles. The center button is for Looking Front Up for following the enemy! The slider on the stick base would be nice for RPM but it's quite easy to hit it accidentally, making you wonder why WEP doesn't work!
On my throttle (an older TM model) I have the Vox tangents for Range and Squad, a button for Looking Up to combine it with the views on the hat, and WEP.
I've assigned Flaps Up and Down, Engine start, Gears, Bomb (Secondary Weapon), Weapon Select, Bomb bay Door, Damage etc. on the buttons but I usually find myself hitting the keyboard for those.