[douglas]

Here's what I do, and it works pretty well in my experience:

No master computer
Max quantum engines
Solar sail
quantum reactor
multiplex tracking
combat sensors
ECM
scattering armor
stealth armor
crystalline armor x10
emmissive armor x3
phased shield generator
heavy mount shield depleter
heavy mount APB x4
PDC x3

If you're willing to pay the cost for a master computer, you can add another shield depleter or take off a PDC or multiplex tracking and add another APB. I include three emmissive armors because the emmissive ability greatly increases the durability of this design, but the emmissive armor is much easier to destroy than the rest. The 10 crystalline armors are not something you can compromise on - you need all 10 to get maximum benefit from the shields from damage ability, and if I had space for them I'd add spares. For this reason, baseships might actually not be a bad idea, despite their 40% defense penalty.

Edit: If your primary opponent is using lots of organic armor instead of shields, the shard cannon might be a good choice as main armament. Make two designs, one with standard weapons and one with shard cannons and try them both out in the simulator.

Edit2: Your opponent is religious? In that case, you may want to strip out the stealth and scattering armors, and maybe the ECM as well, and replace them with a spare crystalline armor and another big gun. Just be careful to use such a design only against your religious enemies unless you don't have a choice.

Edit3: Oh yeah, if you can tolerate their slower speed, baseships are definitely the way to go against religious enemies, as their 40% defense penalty will have absolutely no effect, plus you'll get 500 kt more space and the massive mount, and the space-saving master computer no longer costs more than the alternative.