I wouldn't mind if there were some sort of negotiation 'benchmarks' somewhere. Successes that you could call for, or give out, to influence the actual negotiation.

For example, 10% up front - 1 success.
25% up front - 2 successes.
50% up front -- 4 successes.
Payment in nuyen - 1 success.
Payment in certified credsticks - 1 success.
Pay increase/decrease by 10% - 1 success (May be taken multiple times)
Intel/Aid given - 1-4 successes depending on how good it is.

Etc.

Not a hard system, since those are always open for abuse, but, a few guidelines might be nice.

* Johnson A will pay in corpscrip (0 mod), with 10% up front for good faith (1 'buffer') and has some basic intel (1 'buffer')
* Johnson B will pay in Nuyen (1 buffer) on certified credsticks (1 buffer) but is a cheapskate (20% from normal price, -2 buffers).
* Johnson C will pay half up front (4 buffers!) but only in gear (0 buffers) and doesn't know anything about the target's security (-0).

And so on.

Exactally, you could hire any hood of the street to deliver a package across the city for a fraction of what you'd pay a runner team to do it, but a runner team you know is going to make the delivery, on time, without looking into the package, and not cut and run the second someone starts shooting, because for runners, reputation is everything.

As for paying up front, I usually do it if I expect the run to require a large expenditure of money to complete, but only if the runners have a reputation of being trustworthy. I also use it as incentive if the runners ot more net hits on their negotiations than I planned to pay them(usually 1 or 2 net hits will get to the max Johnson is willing to pay).

For reputable runners, I usually pay half up front. If the Johnson can't manage, he pays additional after. If the runners have any rep, they'll follow through (or refund the Johnson) or they won't be working any more. Given how often Johnsons try to screw over runners, or die unexpectedly, paying ahead should be pretty much par for the course.

RAW already has negotiation tests and results handling pay increase/decreases. There is also boilerplate verbiage in all of the missions adventures that detail how negotiate can increase the payout. Oddly enough, even though I point that out to my player every time they negotiate, they never try to get more money.

Usually, the method of pay and when, I just leave up to the preference of the players. Maybe I haven't backstabbed them enough for them to ask these questions?

By the by, in SR1-3 (and I guess SR4?) if you fail on the negotiation test for pay, your pay goes down. To counteract this, the Johnson ALWAYS lowballs on his opening bid. When the PCs negotiate, even a mild failure is an improvement over the initial offer. This prevents the awkward situation of 'I was offering $20k before, but now it's $16k'.