So for me I use and change the standard formula. The base modifier is 3,000, but not every Johnson uses it, it depends on what they are asking, how much money they actually have, who they (Mr Johnson) are, and how much they want the thing done. The lowest a normal run has gone for was 2,000 (orc underground) base modifier, and the highest is their current run which is 5,000, and is the strangest, longest, and arguably most important run they have ever done. Then I allow the negotiation check for +- 100 nuyen net hit, which I never give a free pass on, but the face crushes it every time anyways like +900 average.
I tend to put something difficult in each run somewhere along the line, usually -something- is going to oppose them with 20+ dice at one point, so +5 for difficulty, then the other little mods, well I usually try to include a few of them if logical, so usually they will get +3-4 miscellaneous adds (like outnumbered 3 to 1). When I remember I like to put +1 per game session beyond the first, to make it so that an extended run doesn't feel like cheating them out of advancement (I do +2 karma per game after first), I should note that this is each not split.
On top of this they will sometimes get operating funds (much less, determined by negotiation) or they will get expenses comped, depends how much, depends who, and depends on the roll. In the current run I actually scared one of my players with this. You see Mr. Johnson wants this thing, she wants it really, really bad. It's also a hard, and expensive run, so she gave them 350,000 nuyen in operational expenses, and wouldn't be negotiated into more, because that was all she could afford. Usually not this much though, as I said this is a really important run, in fact the last really, really important run of Act 1 in my campaign (of about 2 years).
I'm probably paying them more than the average as they tend to earn 50,000 - 80,000 per run, but I've seen no issues, they tend to just blow it on cars. (seriously)