GDI Weapons Factory: You need to be careful doing this one. While anything is inside, they can be killed by producing vehicles. ANYTHING. Evertime a flame tank goes in the producing area, i get to the nearest PT and buy a hummvee (as it's the cheapest unit...) so that the flame tank is instantly destroyed, and the person is killed.

Base defences: these are hard to destroy with beacons unless you have people backing you up, especially the oblisk. The AGT is easier to destroy because it's so large inside, IMO.