The Cube4 base board PCB has a number of breakout regions that you can use to attach your own devices for customising your projects.
Once your Cube4 is assembled, these regions are all accessible from the bottom. You can view the Cube assembly guide here.
For full details on how the Cube4 is wired up, see the schematic PDF on github.
This male right-angle connector provides power and ground, two digital pins, and five analog pins (A0-A5.) You can use these pins in your sketches for analog inputs, ie:
byte x = analogRead(2);
However you can also use them anywhere you use digital pins, ie:
Microcontroller to LED Driver
These pin holes provide access to the pins that the microcontroller (Leonardo compatible Atmega32u4) uses to drive the LED display. Usually you don't want to connect anything to these pins, unless you want to drive the LEDs directly from an external controller. The schematic PDF has full details of these connections.
Note that the holes labelled A0-A3 here stand for "Anode Driver" and are not the same connections as the Analog Pins on the edge of the PCB.
Serial & I2C communications
These two pin headers provide access to the hardware serial RX (digital pin 0) and TX (digital pin 1), and the i2c SDA and SCL pins, as well as power and ground. This makes attaching i2c peripherals to the Cube4 quite easy.
For i2c peripherals, if you connect devices that don't contain their own bus pullup resistors then you will need to solder 4.7K (or similar) resistors in the two spaces marked on the PCB as "SCL PULLUP" and "SDA PULLUP".
For serial communications, if using the hardware TX and RX pins provided on these headers then this is referenced as "Serial1" in your sketches. The normal "Serial" device is the built in USB CDC device.
XBee is a common socket format for lots of wireless devices. The Cube has PCB mounting holes for an XBee socket. These pins are not connected to the rest of the board. Lots of XBee compatible devices use different combinations of pins for different functions, so this allows you to wire the particular connections you need.