The intent behind a computer controlled ship is to turn as much of the operation of the ship as possible over to computers. Crew members push buttons or make voice commands, and the computer makes it happen. In the event that there is a manual override, it is mearly a button to tell the computer to do something it was suppose to do anyway, or a set of controls to tell the computer when to do it. Much of the inter ship communication is also handled by voice command relayed through the computers as well.
If taken to the extreme, the computer controlled ship would not have a crew, only passengers who sit around and do what the computer tells them to. Fortunately this extreme does not exist, and designers must strike a balance with manual operation.
Advantages to the computer controlled ships are that they take away much of the possibility of human error, and eliminate small mistakes.
Disadvantage of the computer controlled ship, is the computer. If anything goes wrong with the computer, the crew has a lot fewer options since the computer that did most of the work is not functioning, and they do not have the ability to do it without computer assistance. Also, all anyone needs to do to take control of the ship is to take control of the computer.
[Star Trek; 2001:a Space Odyssey]
Manually operated ships are the opposite, while they still have computers, the computers are mainly used for complex calculations, or to run mundane tasks that are simple and routine. The main control of the ship is done by the crew, who push buttons, pull levers, and open valves to accomplish the ships functions. Wires and microphones replace the voice activated communication systems of the computer controlled ships.
If taken to the extreme, the manual controlled ship would have no computers at all, with all mathematical equations and course plotting being done by hand. The extreme example of manually controlled ships, fortunately, does not exist, a balance must be made with Computer Control.
Advantages to manual controlled ships are an endless supply of back up systems. The crew knows how the ship works in intimate detail, and can afford to be creative to find new ways to accomplish the desired effect. This is especially useful if the ship is damaged, and the standard systems are off-line.
Disadvantages is that a larger crew is needed to run the ship, and the crew must be well trained, which is expensive and time consuming.
[Yamato/Star Blazers; Battlestar Galactica]
Some Organicly grown ships are "alive" and have their own sense of self. These ships can basicly control themselves, but need a captain or pilot to guide them, but the ship itself takes care of almost every facit of maintaining and running itself.
Advantages to organicly controlled ships are their effeciency. They need smaller crews and make fewer mistakes. They are also more intelligent, maintain a greater awareness of the space around them, and have a level of instinct.
Disadvantages are that they may not do as ordered if they feel threatened. They may need some convinceing if they do not trust their pilots or captains.
[Farscape]