I used to think Siege Towers were great, but I've found I get little use from them since they are kind of slow (and speed boost immune), and short ranged.
I've found that for the lower marks, I get the most use from Implosion Artillery. They aren't too robust, but they have a very nice range, so they augments the fleetball nicely and get in on the action far more often than the slowpoke short range Siege Towers do. And while those .25%'s and .50%'s for damge sound wimpy, a capful or two of them adds up and they can do significant damage to the bigger enemy stuff like golems, dire guardians, or wormhold guardposts.
No one mentioned Martyrs yet, either. I don't build a lot of these, but I like to have a handful of Mk 2 and Mk 3 ones available. They are really useful for "fishing": clearing out the clutter around wormholes the AI has camped out at with hundreds of ships. I can push a few martyrs through the wormhole, slurp up scores of units, and pop back to my side for the fleet to clean them up. Lather, rinse, repeat.