I WAS going to post my victory over a Dominator, but that just seems trivial. Anyway, I am currently in the process of trying to best a Doom class ship. I am quickly discovering that this task my be impossible thanks to the two heavy blasters that are almost always in range thanks to their hefty arc. Wish me luck!
*UPDATE* After 20-30 attempts the best i have gotten is to hit the Doom with 1 annihilator rocket. MAKING PROGRESS!!!!
*UPDATE #2* After a further 30-40 tries i have been able to get the Doom to 1/2 hull until I ran out of missiles. I have decided to admit defeat. I will leave my strategy below so that others may learn from my mistakes.
Spoiler
My most successful strategy was to attach an annihilator rocket pod to the large forward missile mount and rain rockets at the Doom. The AI would cloak the ship any time it felt threatened by the rockets, thus generating flux. Once it overloaded i would spam either torpedoes or harpoon missiles until (hopefully) the Doom was destroyed. Unfortunately due to the high flux dissipation rate of the Doom the overload only lasts a few seconds. When it comes off of overload your best chance of surviving is for the two heavy cannons to not be online. To attempt to counter this i installed two ion cannons to the front mounts. I have yet to survive past a single overload due to either running out of missiles or getting caught out by the superior speed and maneuverability of the Doom. I hope my trials will help you to defeat this monster. Good Luck!