NES: 2 buttons (plus start/select)
SNES: 6 buttons? (plus start/select?)
Genesis: 3 buttons (acutally 6 with the upgraded controller) and start
SegaMS: no idea
C64: 

? See what the games you want need.
I'd guess that 6 buttons is what you need for consoles. I'd just do the 7 button layout that is like mine. Neo Geo is well worth it. You don't need analog. I'd you those Mag Stik pluses.
If you'd expect to have alot of people over, consider a 4P CP. If not, just save the money.
Beyond all this, see what your musts are for Mame. I kinda regret not doing a trackball. Thing costs big bucks though so I can't so I am that upset.
I'll chime in. My cab uses 8 buttons per player.

I got a shot of my panel before painting it, mostly because I was excited to see how the controls would look in the panel.

Each player has six colored buttons, the white player-start button, and an extra black button, for a total of eight. On console emulators, the white button is for start and the black button is for select/mode. The third black button in the upper left is ESC. This setup works wonderfully for Mame and for 8-bit and 16-bit console emulators.
Speaking to the buttons each system needs:
NES: 4 buttons - A, B, Start, Select
SNES: 8 buttons - X, A, B, Y, R, L, Start, Select
Genesis: 8 buttons - A, B, C, X, Y, Z, Start, Mode
SMS: 2 buttons - 1, 2 (the 1 button doubles as start IIRC)
C64: 1 button on some, 2 on others, plus a keyboard. I'd forget about putting this in a cab.
The trackball is the X-Arcade USB / PS/2 assembly. Costs a mere $60, works great, and I love it. I believe it's the same assembly used in their Tankstick.
If I had to do my control panel again, I believe I would move my extra black buttons down closer to the colored buttons, going for that 7-button layout that Ragnar mentioned. It would certainly be more conducive for 4-button NeoGeo games. Aside from that I'm really pleased with how it turned out.