Although it's expensive ($60 - Ouch! ), take a look at REXwireless' Idea Matrix
. It's designed to manage files and documents. If you create a folder for each patient you can import emails about that patient directly into that patient's folder. All correspondence, data, notes, etc., can be stored in one spot for easy reference. Highly customizable, online backup available, and a 14-day trial.
I love REX's stuff. It's expensive, but it's all professional-grade. I rely on Idea Matrix and ToDo Matrix.
The downside of Idea Matrix is that it stores all your files in device memory. No option (yet) to use the media card for storage. I'm told it's a security thing, but having the option would be nice. Maybe in a future version. Simple text files don't take up much room, and the new generation of BlackBerrys have more internal storage, but with 500 patients/folders and several documents in each folder you could be talking about several MB of data.