All the GPIO (General Purpose Input/Output) pins are broken in into two locations. The pins are connected to the 0.1" breakout pins as well as the terminal blocks. The pins are labeled by their 'names' if available and their GPIO # if not. http://elinux.org/Rpi_Low-level_peripherals has a lot more details on what pins can be used for additional purposes (for example, the SPI pins can turn into GPIO's if desired.
There's an SOIC breakout area in the bottom left, handy if you have an SOIC part you want to add. In the bottom right there's a 4-pin terminal block with 4 x 0.1" spaced pads right above it, these are for 'free wiring' - they aren't connected to any GPIO so useful if you want to simply connect some wires or sensors that don't go directly to a GPIO/power pin
If you want have it inside a case, we suggest one of our Adafruit Pi boxes (as long as the top is removed)