Use backstabbing Johnsons. Give them a tough run, where they get ambushed, and then the Johnson won't pay them - doesn't even show. Just another ambush. Then they have to hunt him down, and he's trying to flee the country. If they cut their losses, they're still dealing with the label 'terrorist', and a lot of airtime. If they skip town, they don't have as many contacts, the area is unfamiliar, and every local criminal group is going to be pushing them around. Even if they only take one or two damage every encounter, if you don't let them heal for several combats, they'll be feeling the hurt.
Even if you aren't kicking them out of town, there are options. Paracritters can be horribly nasty, for example. Just watch them try to soak a Sea Wolf nomming on the Troll's face - or his weapon. If you send them hunting, expect them to have to lick their wounds. Never send just one paracritter, never forget their abilities, and they should be sweating pretty heavily.
Drones can be terrifying. You can send in dozens, for pretty cheap, it's expected that you can coordinate them, since generally a single Rigger is commanding a small army, maybe with two or three buddies to back him up, and that means that on each of the Rigger's IPs, they're sending about ten or twenty shots at the party, from whatever angle you please - up above, sliding on that overhead rail, or below, sliding out from a bunch of crates. Use a bunch of Micros, which are absurdly cheap, and harder to hit - a dozen Cyberspace Designs Dragonflies set up to kamikaze will lead to a brown pants moment. Or, you know, just send in a few attack choppers, where you DO have to kill the chopper, not just the pilot, since the pilot is a few hundred miles away, and sitting behind five or so IC.
Explosives are fun.
Shedim. Shedim can do some real damage.
Ares is always playing with Bug Spirits. An outbreak in a secure lab is a good time to call in a Runner team, to see if anything can be salvaged before they nuke it.
Snipers. Not just one or two within five hundred feet, more a team of twenty scattered over ten or twenty miles, hidden by every means possible, guarded by several troublesome measures like Drones and mooks in closets, and explosives. If they're a real threat, and someone wants them gone, but can't do it with a single ambush, they'll call in measures like this.Snipers have some nasty ranges - exploit them, have snipers moving from their spot after shooting, have them use smoke and mirrors, comm calls and fake drops, to confuse, disorient, and delay the party, while they fire again, and again, and again. Have them take shifts, so that every twenty shots or so, they have full edge again.