My setup is an unorthodox setup but what would be an orthodox setup really? Anyway, It goes something like this for FCEUltra:
Controls Save/Load Other
-------- --------- -----
B = z | Up = p Save = q | Load = w Auto-Hold = u | Input Display = ,
A = x | Down = ; State 0 = F10 | State 5 = F5 Clear Auto-Hold = i | Frame Display = .
Select = c | Left = l State 1 = F1 | State 6 = F6 Turbo A = s | Frame Advance = Spacebar
Start = v | Right = ' State 2 = F2 | State 7 = F7 Turbo B = a | Toggle Read-Only = Shift+8
State 3 = F3 | State 8 = F8 View Save Slots = ] | Turbo Speed = Tab
State 4 = F4 | State 9 = F9
Any other Emulator is setup in a similar manner. The reason I don't use the arrow keys for the directionals is so I can press more buttons down at the same time while advancing frames at a time instead of having to resort to Auto-Hold so often when all I want to do, for example, is press up and left while advancing frames. I used to have the States set on the line of numbers but SNES9X's default setup is different so I compromised to stay consistent (plus I like being able to disable back/foreground layers/sprites and since SNES9X's number line is setup already for that I see no need to remap them).