For me it all depends on who the player piss off 
...
I have also used corp security to come after them after a bad run, or KE if they are making an ass of themselves on "protected" city streets. (cause KE couldn't give a rats ass what happens in the barrens... as long as it stays there!)
That's the great thing about SR, the players get to "choose" their antagonists through their own action / inaction. 
Very true; +1.
For me, it all depends on how the game is leaning, and what sort of mood I'm in. I tend to run what I myself want to see get the crap kicked out of -- insect spirits, snooty elven pricks (from either the Ancients if the PCs are comparatively weak, or from the appropriate Tir if they regularly kick ass), a particular corporate Johnson and his minions in both light and shadow, Aztechnology (always good for a
laugh scream), whatever. I like kicking them where they aren't looking; suddenly their team safehouse is no longer in the street gang Buzzkill's territory, now it's in the territory of the Dom Nok Seoulpa Ring, and boy are they in it up to their necks
now. Or almost as bad, the Buzzkills -- did I mention they're the ones hired to provide 'security' for the safehouse? -- need the team to help them against the Dom Nok before they get wiped out.
Change it up. Do three runs in Downtown Seattle's high-tech razor-edged shadows, then throw them to the wolves while running guns into Cascade Ork territory, where the shadows are much fuzzier. Let them pit themselves against Renraku's vicious secret battle to recover the contents of the secret Sub-Room 154-322a in the
Arcology ACHE for several sessions, then interrupt their down-time to deal with a 'this ain't a run, this is daily bloody life' when an anti-consumerist anti-tech anti-urban group of young tribal shamans conjure dozens of spirits to rend their way through a high-class mall in Bellevue.
Keep the suckers guessing, and they'll come back for more.
