When you track time with Screenshot Monitor, you often work on a task defined in one of a dedicated project management applications (Basecamp / Asana / Pivotal Tracker, etc). Screenshot Monitor allows you to add a reference to that task’s ID in a very simple manner. Add a text prefixed with “#” like #245 (where 245 is the task’s ID in another app) to the notes – and ScreenshotMonitor will pick it up and place it into a separate “Ref #” field when you export your report to Excel (Detailed report only) or access your data via API. 
The reference does not need to be a number – it can be any word starting with #.
Another way it is often used is to add into the notes common tasks or categories like #support, #meeting, #UnitTesting, etc. When managers export it to Excel, they will get these categories in the “Ref #” field. This make it easy to get a summary (using Excel pivot tables for example) of how many hours was spent on each of this tasks/categories. Most of the users will probably never use this, but if in addition to Projects and Notes you need categories/tasks – this mechanism gives advanced users a very flexible and easy to use tool.
Actually I think most of your users will want integration to project management apps. This is the main thing that’s keeping me from signing up!
Michael, I agree, while probably not most, but many users would appreciate the integration with project management apps. However given a choice of sloppy integration (like many similar products have) or solid core features + simple to understand integration like described in this post, we will first invest our time on a perfect core before considering the integration.