Coefficient
Coefficient is a scalable open source project based collaboration platform that can run in J2EE and web application containers. It currently provides basic collaboration tools as hot deployable modules. It also provides a workflow engine to help guide projects through their development cycle.

Data Share
DataShare is network application for clients that wish to share data using a central server-> DataShare. DataShare is written in Java, and allows clients to share data (send and receive) without having to know anything about the other clients. It is envisioned that DataShare will be used in collaborative type environments. A client called Rendezvous is already written and available to use DataShare. Rendezvous allows multiple users to simultaneously collaborate using chat, paint, desktop sharing, and audio-video conferencing.

ivata op
ivata op is a free Groupware/Exchange/Intranet system.

JETeam: Enterprise Teamwork
JETeam is a J2EE application that aims to help members of a team working together by offering enterprise services (follow ups of tasks by managers or developers, notification when the status of the project change and so on) and is 100% pure java.

Lucane Groupware
Lucane is a free groupware platform written in Java, designed with extensibility in mind.

Open-Xchange
The Open-Xchange Collaboration and Integration Server Environment allows you to store appointments, contacts, tasks, emails, bookmarks, documents and many more elements and share them with other users. This environment can be accessed via any modern web browser and multiple fat clients like KDE Kontact, Ximian Evolution (announced), Konqueror, Mozilla Calendar and many more. Every 3rd party product can access this application over many different interfaces like the WebDAV interface (XML), LDAP, iCal and HTTP(S).