I've never ran a large Shadowrun game, but I have run a game with as many as 14 people for another game which shall remain unnamed because I friggin' HATE level based advancement. Anyway, here's a few things I've learned.
1) This is the MOST IMPORTANT suggestion I can give you. If you ignore everything else I say here, fine. Just remember this. USE MINIATURES. I don't care where you get them, I don't care if it's just quarters or paper markers or if you have the entire Ral Partha line of figures hand-painted with varients. Whatever. You'll find combat takes half as long if everyone knows where all the other characters are at all the time. I personally believe that every DM or GM of any game that involves combat even once a game should own one of the large vinyl mats you can write on and wash off. They're invaluable to sketch out buildings, cover, etc.
I'm going to repeat this because it's that damn important. USE MINIATURES. In these days dominated by clicky games and other cheap minis, there's no real reason not to have some. Buy a couple of boxes of MageKnight figures, the D&D minis, or even just print out some paper tokens and glue them to posterboard to make little stand-ups. Just use SOMETHING. If you've ever had the problem of every person in turn asking "Okay, where are all the bad guys at?", you'll know how invaluable minis are.
Also, everyone will drift during combat. They take their turn, then they pay attention to the next person's turn, then they TRY to pay attention to the next turn, then they think of some spell they need to look up or someone mentions some movie or something and they're gone until you call out their name and say "Okay, roll your body." If you use minis, you make it that much easier on everyone as they can take a quick glance at the board and get at least a basic idea of what's going on.
2) Limit it to 8 people at MOST. If more people want to play, have a sign-up list on a first-come first-serve basis. If you really want to accomodate more people, run two games. You can run a larger game, but you will bog down FAST. Also, challenges that you thought were hard become laughably simple the larger the group gets.
3) If you ignore suggestion #1, make sure to have an assistant. Even with only 8 people, an assistant is a great help. This person can also play a character, but make sure they have a firm grasp on the rules and can help you adjudicate in combat situations. Your assistant is best for playing the decker, as they are less likely to be involved in combat and generally, if they want to play a decker after reading the rules, they'll probably know the rest of the rules pretty well. An assistant is INVALUABLE. If you have someone else keeping track of intiative and where everyone is, then that's less you have to deal with and it speeds everything up.
4) Groups of identical enemies make a bigger threat than a single very strong opponent. This isn't as big of a deal in a game where most combat is ranged, but if you have even two melee fighters in a group, they're going to run up to the NPC and everyone else is going to have a hell of a time hitting him/her. It's also easiest if the NPCs are identical because you don't have to remember which one is which other than which NPCs have taken damage of some kind.
5) Regardless of what others say, I find that combat-based games run better with a large group. People will tend to have more fun in a large game if it's combat based rather than roleplay based because inevitably, one or two characters will dominate any particular social situation, leaving the other 6+ people sitting around trying to get a word in. Imagine trying to carry on 8 conversations at the same time. That's what it's like trying to roleplay a social situation with 8 players. Combat may run slower with more people, but at least you're going to be assured that each person is going to get a turn.
6) Make sure your players are there to play. The larger the group gets, the more likely it is to degrade fast. Someone makes a smart-ass comment, the entire group laughs. Someone else makes a funny movie reference, everyone laughs. And then you suddenly look up and find that half the table is talking about the movie while you're trying to run the game. The easiest way to deal with this is to make sure no one gets bored. If they aren't bored, they're less likely to stray from the game.
7) Do NOT do decking or astral survalience unless you have an assistant GM. The times when I lost more players to other conversations at the table playing D&D is when the rogue(s) scout(s) ahead. The rogue is off doing the recon mission, and your attention is solely focused on him/her. Everyone else gets bored since their character isn't involved, and they go out for food or call their girl/boyfriends or start trading Magic: The Gathering cards or something else. It's one thing when you have 4 or 5 people and one of them is doing something on their own. It's another completely when you have 7+ people sitting around waiting for the mage to wake up.
Do NOT split up the group if you can help it. Of course it's hard to do, and someone's going to say "Okay, the four of us are going left while the rest of them are going to go right." If this is unavoidable, just call a break for the other players. They're going to take one anyway, but if you give them a set time (try not to take more than half an hour and NEVER more than an hour), they're more likely to stay in the mindset of the game when it's time to start their turn. And make sure to give the first group a break as well while you deal with the second group. This can also work for astral recon/decking/whatever if you have to.
The Abstruse One