Maybe your players won't ever try for a Bloodzilla, and I'm reasonably certain they wouldn't set up a ritual assassin circle... not without the GM handing them a bunch of really really two dimensional NPCs*
But you can bet they will go for the mini-gun troll tank of doom. You can bet they will be calling down the biggest baddest spirits they can get away with. You can bet their riggers will have drone armies, and the mage will spam stunballs if he thinks he can get away with it. The face adept pornomancer will put in an appearence and one player will be tossing out twenty dice pistol shots four times a pass^
Get one of these characters in your game and things will head south fast. Get two or even three and you might be tempted to toss up your hands, declare them all living Gods and drop a Thorcow on them... maybe two, that Troll is pretty tough.
Have no fear, for Obi-Spike-Wan is here to share that most uncommon of things, Common sense.

Now, to start with I'm not going to take the tack of 'kick the bastard from the table' or 'houserule it away' or any of that nonsense. Those are hammers and we're working with porcelain here... or something like that.
More, those are out of game solutions to what is an ingame problem. Yes, virginia, an in game problem.
In general I prefer to use two principles when dealing with problems. Escalation and resources.
Escalation: The players stomp around with a pack of farce 12 spirits as backup? Eventually, and by that I mean sooner rather than later, someone is going to set up a way to stop just that. Be it their own pack of farce 13 spirits or maybe just finding the true names of the spirits the players use+. Have a Troll that can beat a Citymaster in a headbutting contest? The other guys WILL have anti-tank rockets just for him. The more extreme the character the more likely this sort of escalation will happen, simply because it is that extreme. That level of 'power' is damned uncommon and people WILL learn about it in short order, and then take steps to fix it. One fun trick is to simply copy the PC's character sheet and use them as Nemesis.
This brings me to the second point.
Resources: There are at best half a dozen characters. There are billions of metahuman NPC's. Anything, any rule, that applies to the characters can apply to any one of those NPCs. And if the player hasn't totally topped out, somewhere is some bastard who can beat him, there's just too many people for that not to occur. Worse, all those corporations, governments, mafia types.... they all have more money than the players and a vested interest in not being challenged. Ares might not mind the occasional shadowrunning team beating their security, but they damn sure will object if it becomes known that they can not, no matter what, stop this one team. Without the benefit of total anonymity (and sorry, Tank troll, or Loamage or Pornomancer Elf just don't qualify for that sort of thing....) Ares WILL move heaven and earth to prove that they are the biggest dog in the yard.
Of course, this sort of thing can simply lead to further escalation from the players, particularly if handled poorly and used exclusively. Players like to match force for force, and object if they feel the GM is 'cheating' to beat them... even if cheating means that some security mage targets TankTroll with mind control spells exclusively. This brings us to part two.
In some cases it is necessary to provide disincentives to the players to prevent totally borked characters. Again, I have a couple of buzzwordy ways to do this: Exploitation and Enforcement.
Exploitation: This one is shockingly easy. Give me 2000+ karma and an unlimited budget and I can make a character that is good at everything... expert at everything, that is. Anything short of that and the character is going to have weaknesses that can be exploited, so exploit them. TrollTank is probably a drooling idiot, and drops like a punk to the weakest of spells. Bring more casters and the party counterspeller will fail him, probably at the worst time. Use a sniper against the counterspeller... hell, start using snipers more often if the PC's are that dangerous in a fight. It might be a bit much to ask, but play smarter than the players. Extreme firepower makes 'em cocky, use that against them. Put them in situations where they simply can not bring their most borked aspects to bear. Make the technomancer have to fix a broken computer (hardware) before he can hack it for the paydata on it. Sure, he'll succeed, and still do so using his borkedness maybe, but I doubt he's optimized for Hardware tests. TrollTank is useless when stealth is needed. Pornomancer gawps stupidly at the incoming wave of drones, as does the mindcontrol mage...
Enforcement: Anyone who has gamed with me, and probably a few of you who have read my posts, will know that I like to take it easy with rules, I'm all about just running with it. Thats right, Enforcement means 'Ruthless Enforcement of the Rules', something that absolutely needs to be done to deal with potentially borking characters. Technomancer spends every waking moment registering sprites? Legal, even feasable, if not exactly realistic. No problem, start keeping notes on how many sprites he has, how many services they've got, then bring on the 'long run' where you burn all that off him. Ditto Minigun toting 'TrollTank'. Say, who gave the TrollTank that minigun after all? Make him have to work to get more ammo while the other players are just marking off nuyen between runs, if that. Same with PACman. Got a mage working to become 'Bloodzilla Boss'? He still has to learn that bloodmagic in game, don't he? That's some serious legwork, and even more serious negative attention coming his way. Got Lucky Edgy in your game? Who controls when Edge recovers? You do. Lots of the most borked character examples seem to be designed with high edge in mind, even for 'casual rolls'. Edge is cool, yo, but it don't have to be free as well. Once again, bring on the 'Long Run', the multi-session run with no downtime where expendable resources are burned off. An easy way to do this is to have the target of a 'difficult' run turn the tables and start actively hunting the runners. Such heavy hitters are visible, and putting the players 'on the run' is a perfectly valid 'adventure' for a group of professional criminals. If it isn't, your players are spoiled brats.

When all else fails you still have one last resource before resorting to Thorcows. It is the awesome power of the GM fiat. Rules don't provide for a 'no-mana zone' where farce 12 spirits can not abide@? Make one. Put the Mcguffin in it. Don't tell the player unless they check or step in it. Want an unbreakable encryption? Make something 'uncrackable'. Just don't use it for everything. A one use device, say, not a datafortress. Player makes all the dice rolls necessary to become a bloodmage and prepares to summon Bloodzilla? Declare that he has 'won', his character is now an NPC feared, respected and hated by everyone. For bonus points, hire the PC's after that to 'assassinate him before he tries again' and run him as borked as the player made him.
Disagree with me? Tell me why. Think I don't know what I'm talking about? Challenge me. Give me a legal character, give me an expirenced character and I'll tell ya how I'd handle it. If I gotta pull out the Fiat, you win, I was wrong and we can continue chortling over our badassatude. No houserules~, no 'I don't use that book/line'.
*More than usual, I mean. As in 'slavishly devoted to furthering the PC's goals for no reason'
^ Don't ask me how, I'll just lie. I totally made up that number, but I can 'semicasually' get close to it.
+ I mean use the system to remove the assets from player control. Unsummon, whatever, and stack the situation in the NPC's favor. I figure Farce 12 spirits are uncommon enough that the player can not logically argue he is using new spirits for every summon... The existance of free spirits is proof enough for me that spirits are as 'real' as any other NPC.
@ I seem to recall reading of such a rule actually, but I'll be damned if I know for certain it exists, much less in this edition.
~ A houserule either requires a dice roll or negates/alters existing dice rolls. Spirits as NPC's, for example, isn't a houserule, its a method of RPing something in setting, as long as I don't force, remove or alter a roll from RAW. Likewise, where the RAW requires interpretation due to vagueness or debate over meaning is not a houserule either. A wildly inaccurate(unresearched recently) example: casting a spell through a ward at inanimate object 'focus' of the ward to bring it down easier than actually bringing it down. This was debated alongside ritual assassin circles a while back, and to my dim memory there is no rule that says wards have to be cast on a easily identifiable focus object. I would treat such an attempt as a flashy way to 'attack the ward' per the rules. Not a houserule, simply applying the rules available to me in a vague instance (the entire Ward debate was illustrative of houserule/not houserule in that almost any interpretation of the wards vs. ritual spell attacks could be called RAW or a Houserule by the opposed party). To sum up: Interpreting the rules in a favorable way is not houseruling, its the GM's job. Making some shit up or altering the rules in some meaningful way IS (fer ex, changing matrix rules to attribute vs skill. Altering the encumberance table, adding a trousersnake table to affect seduction rolls...). Caveat: I reserve the right to make simple, on the spot, rulings to cover areas of 'no rules exist'. Fer ex: If there is no rule regarding sleep, that does not mean I have to allow players to function as if sleep, and lack of it, did not affect them. Thus I can 'on the spot' say that only 16 hours a day is useful for summoning, compiling, hacking etc, and I can apply penalties to players who attempt to walk across the sahara desert without food or water. However, I will endeavor to avoid doing this in this thread unless someone gets stupid with it.