I have used both at the same time. That is, I had both Eclipse ".project" and ".classpath" and IntelliJ project/module/workspace files in the same project so that editing could be done with whichever IDE was handier at the moment. And I did my production builds using
Ant on a non-GUI Solaris machine after developing in an IDE on Windows.
I can live comfortably with both IDEs, though I prefer Eclipse myself. IntelliJ I think is friendlier to line-level developers, but Eclipse has the ability for me to debug multiple cross-communicating apps with less button-pushing.
I've used Eclipse with SVN and CVS (in fact I have both types of project on the machine I'm typing this on). No problem. Well, not much. SVN is a little annoying sometimes. If I'm not mistaken, JIRA hooks into Mylyn.
Both Eclipse and IntelliJ support JUnit. I've found it easier to do JUnit under Eclipse, however. Then again, I'm a release behind on IntelliJ at the moment.