I finally got my favorite IDE Eclipse working with Cytoscape. Here are the steps I took:

1. Create a new project using "Checkout Project from CVS", using the information at the bottom of the Cytoscape download page.Make sure you create a new Java project after checking out from CVS. Designate src as a source directory and use a name other than bin for the project output directory (there is already a bin directory in CVS).
2. Add all the JARs in the lib directory of your new project. You should then have no compile errors.
3. Create directories called fake_src, fake_src/cytoscape and fake_src/cytoscape/view.
4. Symlink or copy the resources directory to fake_src/cytoscape.
5. Symlink or copy the images directory to fake_src/cytoscape and to fake_src/cytoscape/view.
6. Symlink or copy the help directory to fake_src/cytoscape
7. Modify the build properties of your project and designate fake_src as a source directory.
8. Create a "Java Application" run configuration that uses the cytoscape.CyMain as the main class.
9. Run it!

The above steps essentially duplicate the actions in the run target of the ant build file, except for the compile and copying of resources/images/help files that Eclipse does for us automatically.