biggest tip I can give:
keep the game moving. this applies for every aspect, combat, legwork, buying new gear. even when every last member of the team is doing their own thing, make sure someone is interacting and moving toward a goal at all times.
One of the quickest ways to lose a groups focus is to have nothing happen for five minutes.
Learn the rules of everything an npc is going to use before the session starts. for things like spirits, gear, etc get the stats out on paper or notecard or into your laptop (if you use one) before the session starts, the last thing you want to be doing is looking these things up midgame.
If you can't remember the rules for something you want an npc to do: don't do it, or if you have to- wing it.
if you don't know the rules for something a character wants to do (and they don't remember/know them either) wing it. if it's a matter of life or death for a PC- then go ahead and look it up. if you wing it, remember to be consistent for the rest of this session. then look it up after the game ends.
Remember that NPC's have families and goals and fears and hopes and dreams too. don't get caught up in the stats, and roleplay them as much as possible.
Encourage your players to know the rules that affect their character. you'll be amazed how much this speeds up the 'slow' parts of the game.
Remember that anyone with a gun is potentially lethal to a PC, no matter how much karma that PC has. Remind your players of this (ingame preferably) periodically too.
try to work in as much setting specific detail as possible. if you run in Seattle, Make sure you mention things like the sound, the space needle, Have a run in the redmond barrens that goes through portions of the Microsoft compound. Make sure the players KNOW they are in seattle. don't let the setting become AnyCity, UCAS.
as far as general tips with respect to the game system.
Shadowrun to me is meant to be an uphill struggle. and about anti-heroes at best. Shadowrun isn't about The heroic and ultimately successful campaign to rid the world of evil. nor is the team the 'destined light warriors' of the realm. don't fudge dice to keep anyone alive. NPC, PC, Ultimate Villian. if the numbers say they got a bullet to the head and DocWagon can't respond in time. then they die. (or at least hand of god) Death is Meant to be a part of this game. it takes out the challenge if your players are convinced that the worst that can happen is a new cyberlimb and a point of magic gone.
Don't save your favorite NPC villian either. if the PC's get a lucky shot, clap them on the back and congratulate them. your plot can adapt to fill the gap made by their untimely passing.
oh and final point: you have the last word in everything. if there's a rules disagreement, your decision is final for that session. then go look it up. and bring the exact and correct rule to the start of the next session. Let the players know that any issues will only be addressed after the game is concluded (see the first point about keeping the game moving) rules arguments are only interesting for the people having them.
a bit longer than I was planning. but
I guess I had a lot to say.