I've been using JSTs to connect between components. Here are the pinouts used:

3-Pin JST for Pots

1. Ground
2. Analog In
3. 5V

5-Pin JST for connection from Raspberry to Arduino I2C Bus

1. SCL (I2C Clock)
2. SDA (I2C Data)
3. Ground
4. 3V (supplies level converter LV for Raspberry Pi)
5. 5V (provides power for Arduinos)

6-Pin JST for connection between Arduino I2C Bus components

1. SCL (I2C Clock)
2. SDA (I2C Data)
3. Ground
4. (N.C., Future)
5. (N.C., Future - maybe 12V for servos)
6. 5V (provides power for Arduinos)