The biggest benefit of custom software is that it provides features that off-the-shelf software doesn't. Designing an application with your organization's needs in mind typically leads to an increased level of productivity once the solution is implemented.
If you have a software application designed to increase productivity or address an internal need, its cost is offset by the promise of increased efficiency. If your organization has a need that's specific enough to warrant custom software, then customizing a solution becomes a smart course of action.