The enclosed systems. Consult the technical manual for the avionics being used for the most specific information, the information presented below is only for general reference. 

RF Transparency

If your avionics includes a radio for arming, data transmission, or tracking, the RF transparency of the avionics bay must be considered. An avionics bay made of or containing a large amount of, for example, aluminum, will block most if not all radio transmissions from leaving the bay. To counteract this, use RF transparent materials in the construction of the bay wherever possible:

• Fiberglass

• Paper/Cardboard

• Plastic

• Carbon Fiber (in some applications)

If the material of the avionics bay cannot be changed, then an alternative option is to move the radio antenna to somewhere with better transparency. Some very large rockets affix the antenna to the outside of the rocket's body, or to one of the fins. Moving the antenna away from the transmitter requires special considerations for radio interference and specialized connectors. 

Pressure Equalization

If your avionics includes any systems that use barometric altimeters (common on most deployment and tracking systems), you will need to vent and equalize the pressure of your avionics bay, so that the ambient pressure matches that inside the bay. To do this, a series of holes need to be drilled into the outside wall of the bay. The more holes there are, the better the airflow will be. The sum of the surface areas of the holes needs to be greater than a threshold that can be calculated. For a reference table, and the formulas required, visit: http://www.vernk.com/AltimeterPortSizing.htm.

There is also a nice port size calculator available here.

When placing these pressure equalization holes, it is important that they are not immediately over the top of one of the barometric sensors. The flowing air escaping the hole can trick the sensor and cause it to deploy charges at random times. 

Board Orientation

The orientation of some boards is critical for proper operation, if they use magnetometers or other mutli-DOF sensors to determine spacial positioning. Consult the manual for the boards to see how they should be mounted.

Momentum Mounting

During flight, the acceleration of the rocket is so extreme, that some parts in the avionics bay can shift around. In worst-case scenarios in the past, flight forces were enough to disconnect a battery from its board, leading to an entire vehicle loss. 

When mounting heavy and large components, mount them to a solid substrate (thick wood or plastic sheet), and use a securing method that provides active resistance to movement in all directions. A tightened zip tie over a 9V battery is not sufficient, you'll need at least one zip tie in either direction. Boards should be mounted with 2-4 screws at minimum, and their threads should be threadlocked or otherwise hardened against vibration backing them out.