I'm all about keeping the game quick and simple. As such, I do a few things that are house rules to help this along.
I play the frame damage the same way as Hod. It helps me to keep track of how much damage has been recorded, meaning each cycle on the DAC will always be 10 points damage until the ship blows or there's no more damage points to allocate. There could be 36 points of internal damage and I know I will always be 3 cycles on the DAC and will always end on the 6th column of the DAC.
When we use the ISC and their PPD's, I saw a rules option in these forums that I really liked that further simplified that weapon. It's the one that takes a missed roll and lessens the pulses that strikes your target by the amount missed on the "to hit" roll.
One more thing I do, sometimes, is an all or nothing with my like weapons. The other night I did a fleet action with 5 Klingon ships on my side and 6 Gorn ships on the other. When my C10 lined up for a strike against the Gorn BC, I decided I did not want to roll 9 (I don't remember the exact number but I think it was 9) PH1's. So, I rolled one die for all 9 and then a separate one die for all 6 disruptors. This allowed me to quickly calculate the damage done at that range. Yeah, it messes with the averages, but I like things simple and I'm probably a touch lazy.
The last house rule that comes to mind is regarding the Hydran Stingers. Once more, I like things simple. So the Hydran player must form his Stingers into "flights" of 3 Stingers. If he only has two or four, then flights of 2 stingers each. The flights move together and fire together. When they take damage, the same one is always hit until destroyed. This helps me cut down the clutter on the map and helps keep track of where those pesky fighters are at.
Mostly though, I keep the game pretty pure. Nothing dramatic or game altering and nothing that brings it closer to SFB. As Scoutdad pointed out, if you would like SFB, it's right over there and is an excellent detail oriented game.