Many systems are essential to the operation of any space-borne vessels.
The following items are required for all starships and shuttlecraft.

Fuel System
Fuel (Deuterium) / year
Fuel (Antimatter) / year
Fuel is typically loaded at ports (spacedock) during any stop.  Vessels can use Bussard Collectors to gather Deuterium, and can convert Deuterium to Antimatter if needed - however the process is slow, and used in emergencies only.

Internal Transportation
To get around inside vessels with multiple decks you must have a means of access.
Jeffries Tubes*
* Jeffries Tubes are required for vessels larger than Size 5.
They allow access to maintenance areas and other sites where Turbolifts do not reach.
Smaller vessels with Turbolifts may downgrade to Ramps/J-tubes only, but it must be done at a Spacedock.
NOTE - Downgrading will significantly increase travel time between some areas of the ship in emergencies!

Cargo Areas
All vessels need areas to store items not currently in use - but which may be needed in the future.
Storage Lockers may be of any size and are found on all size vessels.
Cargo Bays / Holds are large open spaces of one or more decks in height usually found vessels larger than Size 4.
Cargo Bays/Holds are usually a fixed size depending on the needs of that particular vessel, and may be adjusted as needed.