You can make the comparison between the IDEs by taking the different components of the reference model in turn than assess how well the IDE toolset being studied provides these services. You also have to look at how these services are used in particular toolsets.
Generally, IDEs are tightly integrated systems and all parts of the reference model may not be applicable. In this case, comparisons would be drawn using:
1. Data repository services. What kind of data management is supported?
2. Data integration services. How well can data be interchanged with other tools and what support is provided for configuration management?
3. User interface services. What facilities are supported to allow presentation integration? How well integrated at the user interface level are different parts of the systems?
4. Task management services. This is really for general purpose environments so is probably inapplicable to Java IDEs.
5. Message services. How do different components of the IDE communicate?