Living Crew vs. Master Computer

It really depends on the amount of research that you have put into the various crew options. To me in the end of the game, I feel it is better to use bridge + crew quarters + life support instead of the MC because it costs less and takes up 10 less kt. The experience bonus is helpful, but an extra 1200 kt of armour is as well. When they are first introduced, they are more helpful because they take less space on larger ships, but once crew quarters can hold enough so you only need one component, that effect is neutralized. On the other hand, with space stations, the crew requirements are steep enough that a MC is advised unless you are going for cost efficency.

So it really depends on the overall strategy. A design with a self destruct device nullifies any takeover attempts, and if it is installed, then the viruses won't have an effect to begin with. Personally, I stick with crews.
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"Light travels faster than sound, that's why people seem bright until you hear them."

Crew experience increases your ships' chance to hit with direct fire weapons. It also increases your chance to 'dodge' direct fire weapons.

I'm not sure if it still works this way, but in SE:IV Master Computers could still gain experience, and since they also get nice bonuses to stack with experience, I always go with Master Computers. IMO, a +20% to hit/be missed helps far more in combat than 1200kT of structure, especially with Stock damage rates late game.

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Give me atmopshperic manipulation cannons, or give me death!

MC does gain XP.

I eventually put both MC and crew on a ship. I like to have crews just in case of the enemy using computer virus and knocking ships out of my fleet. On the other hand, the MC bonuses to combat are significant in the late game.

Early on I put MCs on all ships to save tonnage. When I get lvl 5+ hull sizes, as well as better medical and psychology tech, I replace low-lvl MCs for crews to get virus protection without tonnage penalties. Eventually, when my computer tech is high enough, I'll soak up the extra 40kT for the MC's combat bonuses.

Another good source of XP is the ship and fleet training facilities, which stack (advanced military science.) Must-haves for powerfull shipyard planets.

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"No plan survives contact with the enemy"
Moltke

I started using lots of MC ships because it is slightly cheaper to build. My opponent had lots of ships with boarding troops and I thought my MC ships would be immune because they had no living crew to overcome. I realised the problem with that when he lured me into a storm that negated shields.