A number of my readers have asked me about open source software for clinical research; I recommend taking a look at OpenClinica. From their introduction:
It facilitates protocol configuration, design of case report forms, electronic data capture, retrieval, and management. OpenClinica supports HIPAA guidelines, and is designed as a standards-based extensible, modular, and open source platform.
It has all the right buzz-words: it’s web-based, written using Java, and is pretty simple to use.