When I worked with IntelliJ regularly, it was more like $649. They're definitely suffering when all their competition is free.
On the other hand, they feel that they provide a little something extra for the expense, and I can't argue that they do.
A feature-by-feature comparison of the Big 3 IDEs is probably pointless. I do feel obliged to point out that having a whole raft of function keys is not a situation exclusive to IntelliJ, though. I doubt I use 1 in 10 of the Eclipse shortcuts, but a few of them are probably hard-wired into my hands by now.
On a macro scope:
IntelliJ - fine-tuned for run-of-the-mill Java development. Also has the best GUI designer I've ever seen for Java, which was sorely lacking in such things since the demise of Visual Café with the extinction of the dinosaurs. IntelliJ's Swing designer is a standout in that unlike all competitors, it doesn't employ vendor-proprietary "helpers", which is important to those of us who want to release the end result as open source.
NetBeans - I'm ashamed to say that I'm way out of date here, but NetBeans was where Sun prototyped development for many of its platforms, so it tended to have useful tools that no one else did. And if I'm not singing the praises of NetBeans here, there is no shortage of people in this forum who can and will.
Eclipse - In Java, perhaps the most useful thing about Eclipse is that it's especially helpful when you want to debug multiple interlocking apps. Say 2 webapps, an RMI server and an
applet running and interacting at the same time. Not your average developer's functions, but this is the kind of stuff I do. Eclipse also provides a rich set of plugins for non-Java purposes, such as Python, shell scripts, C/C++ and even COBOL. In fact Eclipse itself is a framework program written in Java whose actual use depends on the plugins installed. We commonly employ the Java development bundles such as Helios, but you can also just download the core Eclipse without development support and use it anyway you like, including as a container for your own plugins.
So which one you prefer depends on what your focus is. And, of course, on what your employer lets you use.