[Suicide Junkie]

b. Use Master Computers. If your master computer is taken down (i.e., virus), it may be subverted.

IIRC, in the latest patch, a destroyed MC is still immune to subVersion.

IF your opponent uses Ship Capture:

Use shield regenerators... even 1 point of shields is enough to stop boarding parties.

a. Use Phased Shields. Forego using many normal shield components.
b. Use Armor. Get to Armor V as a priority.

A: Use phased shields. Any normal shield components must be removed, or they will nullify the phased shield protection.

B:
Armor 5? Armor 3 is the best for hitpoints, and armor 6 is needed for the full 15% ECM from stealth and scattering armor, IIRC.