First of all, are they in a Waiting status or a Pending status? Pending would be recurring reports that are cumulative in nature. We currently have over 13,000 Pending. These are set to go off sometime in the future. If you have only a few users, it would be easy enough to go into the "Manage Objects", drilll into a report and look for recurring reports. Or ask the users.
There is a known issue should the maximum number of threads per Job Server be reached. If this happens, the Job Server refuses any further requests until it has been cleared, but upon completing the load, it never sends a response back to the APS asking for more work. A patch has been included in Service Pack 2, and a separate patch fro CE for the issue is ADAPT00229186.
The way to tell if this is occuring is that you have say 10 Job Server threads available on your system, a baclog of reports but only see a few threads (JobserverChilds) running.
We also have multiple servers and Job Servers running. 2 Quad boxes with 4 Job Servers on each. Running 5 threads per, but have experimented with more.
Another issue to look for is a poorly formed query. We found some that were taking all the threads, running for several hours, and causing a backlog of waiting reports.