I would like to have both Eclipse and Netbeans (with JUnit) installed on one system, so I can be somewhat familiar with both.
Besides GUI development (see "Using both Eclipse and Netbeans"), are there any other issues with using both IDEs on the same system, or even the same project?
There are no issues at all with having them on the same system. However, each have their own project specific files, so using them on the same project isn't seamless. This is made a lot easier if you're using source control and keep your (non-source code) project files separate.
We regularly use both Netbeans and Eclipse. We switch back and forth, between Vista, WinXP, and multiple versions of Fedora of the 32- and 64-bit variety, with no problems. Keeping the project files in version control makes keeping them in sync much easier. We even keep the launch files in the project directory as well. I posted a answer to another multiple IDEs question that describes what our project directory looks like.
Basically, I agree with Bill the Lizard about there being no issues, but disagree about the seamless nature and keeping the project files separate. The only thing we have to do is make sure that we update the build classpath in each project if a new library is added because Netbeans and Eclipse use different files to describe the classpath.
Using the IDE version control system integrations helps to encourage keeping the projects up to date for everyone else.
One thing that makes developing single project in NetBeans and Eclipse is using maven to keep dependencies together. Maven will generate IDE specific files that contain all classpath information, buildpaths etc.
Maven has pretty steep learning curve, but it is worth learning.
Maven is a very good way to keep both IDEs in sync (as suggested). In my experience though, you have to create an Ant build for any given project for the sake of developers not using IDEs. Since NetBeans's build system is based on Ant, it's pretty trivial to just base the entire NetBeans project off of that base build system. A little bit of tweaking in the project.xml ensures that the editor classpath is kept in sync with the Ant build classpath.
Netbeans 6.5 has an improved Eclipse project import which is supposed to sync changes from Netbeans back to Eclipse: http://wiki.netbeans.org/NewAndNoteWorthyNB65#section-NewAndNoteWorthyNB65-EclipseProjectImportAndSynchronization