Energy capacitors increase the damage done by beam weapons mounted on the same ship. Each energy capacity increases the damage done by 10% - this is cumulative, so three capacitors gives a total of 1.1 x 1.1 x 1.1 = 1.33 times the damage.
Maximum damage multiplier
In rgcs on 28 April 1999, overworked wrote...
With an overall upper limit on the multiplier being 2.50. Thus a 10th energy capacitor will increase it about 0.14 from 2.36 to 2.50. A 6th flux capacitor has very little effect since it will modify the multiplier from 2.48 to 2.50.
I've never seen any combination theory where flux and energy capacitors are mixed. Probably fairly meaningless since these limits generally require Nubian hulls and 9 of one or 5/6 of the other make it pointless to experiment further.