Gunships are great counters to catapults. Get a group of gunships with a lot of figters as protection and a way to soak up AA and no more catapults! If your opponent is catapult creeping, then a great way to counter that is to build a catapult just out of range of their catapults. That way if they try and catapult creep any further, then your catapult takes out theirs before it is finished. There's also always the good 'ol nuke or planet smash.
I believe that Scathis recently mentioned the possibility of the Inferno or Vanguard (not sure which, or if both, but I suspect only the vanguard) playing an anti-tactical missile role. It's not implemented yet, but is something to keep an eye out for.
My problem with this is that t2 air structure. they are quick and cheap, and in my experience a handful can protect against huge amounts of gunships. Another thing to remember is that even though it may be *technically* possible to overrun anything with enough army, building such a force is damn hard when being catapult creeped. as a general rule, if they get artillery up first building counter-battery is near impossible as they can snipe it before it is complete. you then send your armies to take the artillery and are usually massacred by laser turrets and walls. okay, fine, so you have to go around. assuming you are on a moon, this is easy, but gets progressively harder with different planet types. (some earth/lava types you simply can't flank the base with a land army, and metal planets tend to have tiny choke points everywhere.) assuming you have the enough of an army left, you go to do that all while your core t2 mexes and factories die one by one. if you can get around and attack, (which is a best case scenario) then you take out the towers (assuming he doesn't just spam walls with the swarm of build capacity at the offending fire base) and then the artillery and bingo, you have cleared up the threat, but are now waaay behind your opponent in mass, and in tech. alternately, you try to take out his Eco to level the playing field, but are still faced with the threat of the artillery. It isn't impossible to take out both in one attack, but it is difficult. the laser defense towers at the artillery position often thin your attack heavily, making further pushes suicide. And let's not forget, your opponent has an army too, and likely a far bigger one. after all, he has the mass advantage. T1 air is near useless against a turtle shell, and t2 flak or fighters can neutralize any attempt to attack via air. Nukes are generally effective, but only if your opponent didn't think to build defense (which is unlikely.) plus, nukes are expensive. good luck building one with most of your starting eco gone from the artillery. I have hit this situation several times in game, and it can be frustrating, but it comes down to the game not being balanced yet. there is no hard counter to artillery of any kind right now aside from a strong offense, and yet there are plenty of counters to such an offense. It is also possible that I just haven't figured out the perfect counter, but believe me when I say I have tried.
"Don't play on tiny maps". I really don't understand why people love playing on maps that are so small, my base starts off within catapult range of yours.