Ahem
Perhaps you guys are taking size TOO much into hand. While in many cases, age equals wisdom, I know many old people who are utter fools. The same can go with big giant warships. A ship that size needs very, very extensive support and technology to keep the gravity of the ship itself stable and to keep it from falling in on itself.

Really, once you reach a certain point. making bigger ships gets too costly, since [in proportion to other, smaller ships] there will be less space for everything, and more space used up for support of the ship.

Really, you'd just have to blow a couple reactors inside the ship [which can't be too far from the hull, since the ship is so big, meaning that there would HAVE to be reactors near the hull to release heat and such, which also makes it traceable due to the massive energy requirements, meaning more heat coming out of small regions].

In other words, these big ships are not actually invincible. Come in with a little ship, send a sublight antimatter missile through the heat release into the reactor, and it should, at the very least, cause a millisecond's worth of electrical unstability, which could very well cause something to short out with the sudden recovery, and make part of the ship collapse in on itself. With the whole something-in-motion-stays-in-motion-unless-an-outside-force-acts-upon-it, this could very well cause the entire ship's demise. While there would certainly be operational pieces the size of regular ships here and there, the effectiveness would more than likely be completely wiped out.

Also, sorry for the absence. My internet received pooped on its own software, and I had to hunt through thousands of shiny little disks for the right one to reinstall it.