Craig,
As far as the 3 objects within a report, I have not necessarily figured a way to pull them all into the report, but I have in the past been able to use 3 objects in a report (using one as a filter). In your example, I am not sure how your model is setup, but thinking based on the objects (Apps, Projects, and Cost Source), I would think that you may be able to do this in leveraging the project & cost source object if you Application ID is within the projects data since the relationship from Projects to Apps is based on the App ID.
Now another piece of information that you could also potentially leverage is using a tabbed report so all the information is within one report, but you could have one tab for one section of the report and a second tab to look at the other piece of information.
Thanks,
Ryan