Shadowrun seems to have a very thorough attitude of "depends". Does the Johnson think the job is worth 3k x (# of Runners)¥? If I'm the Johnson, and I think a job is worth 10k¥, I'll probably try and get someone to do the job for 6k¥, maybe 8k¥. You may notice, I'm talking total pay to the group, let them dicker about how to divy up their profits.
At the same time, from the GM-who-likes-to-keep-people-playing perspective, you need to be paying enough to keep them alive and fed. If the first job pays less than ammo & living expenses, your players are going to revolt. Don't get me wrong, some jobs should have shit-for-pay. And don't forget, just like in DnD, your players are liable to be on the lookout for ways to increase their profit. Just because they're getting the 2 - 3 k¥ from Mr. Johnson doesn't mean they won't find 10k¥ worth of paydata, drugs, or weapons during the job.
Pricing a run, I look at the Johnson's motives and what he knows, not what I, the GM know. If I, the GM, know that the paydata they're going in for is guarded by a trio of spell-slinging drakes, I simply smile a little on the inside. If Mr. Johnson knows it, and intends to let the runners know, too, he's going to expect to pay for that fact. At the same time, if he's ignorant and just thinks it's simple, in-out, rent-a-cop security from Bubba's Security Solutions that shouldn't take more than a night, he's going to pay a pittance.
Price goes up if the Johnson is desperate. Price often goes up if Johnson is hiding something (to keep the runners from asking questions).
Price goes down if the Johnson can afford to wait. It also goes down if he's a conniving son-of-a-bitch who knows what the job is worth, plans on killing the runners once they're done anyways and fully expects to get away with it. Price also goes down if the runners demand payment up front.
All that being said, if you look
around the place, and on
Dumpshock, a pricing guide out of an old 3rd edition book has been making the rounds that gives at least a little guidance.