Need job profitability by rep report (sales - costs), but QuickBooks does not have this report. QuickBooks tracks only gross sales by rep. Want to pay sales people commission on net profit on jobs (net profit, meaning Sales less Costs of Job).

Solution:
Since QuickBooks cannot produce a report like this, below are several potential work-arounds:
Important: Any solution will need to job-based, not invoice (or transaction-based). In other words, we cannot determine net profit on any specific invoices or sales transactions. However, profitability can be determined on customer:jobs. Therefore it is important to always setup a job instead of creating an invoice to a customer (or parent).

Option 1:
Export "Job Profitability Summary" report and "Customer Contact List" report (with column for Rep shown) into Excel. Then run a simple Pivot Table Report in Excel to group by selected Rep.

This option works well, the only drawback is that you have to re-export fresh data whenever you want updated reports. QuickBooks 2012 offers a new feature that allows for updating reports from Excel (but this works only for transaction-based reports and not list reports).

Option 2:
Use the above concept, but with an ODBC tool that lets you sync to/from QuickBooks and Excel. (qodbc.com/qodbc.htm). This would allow you to develop the report in Excel or Access (or similar application) then simply refresh the data at anytime.

Option 3:
Instead of using the Rep field in QuickBooks, use the Customer Type field for the Sales Reps. When setting up a new customer, you would have to be sure to select the appropriate rep. The rep would be assigned to the job, not the invoice. A Job Profitability Summary Report could then easily be configured to show profitability for a selected rep.

This may be your best option, since the calculations are all done inside QuickBooks. The only drawback is that the Rep (Customer Type field) would not be visible on the invoice.