I also had trouble with button combinations, trying to find the best places to assign keys to. Some of my gamepads were all over place in order to avoid an unresponsive frame advance.
My settings are:
1st player
- v for A
- z for B
- r for C
- Caps Lock for Start
- Normal directional pad for Up, Down, Left, Right
2nd Player
- k for A
- n for B
- p for C
- ] for Start
- [ for Up
- / for Down
- ; for Left
- ' for Right
3rd Player (if using teamplayer)
- d for A
- q for B
- e for C
- ~ for Start
- y for Up
- b for Down
- g for Left
- h for Right
I used \ for frame advance. If you're using six buttons for two players, I recommend:
1st player
- x for A
- z for B
- c for C
- s for X
- a for Y
- d for Z
- Caps Lock for Start
- Normal directional pad for Up, Down, Left, Right
2nd Player
- k for A
- j for B
- l for C
- i for X
- u for Y
- o for Z
- ] for Start
- [ for Up
- / for Down
- ; for Left
- ' for Right