For example, in GWT, I can command-click (this is on a Mac) on a GWT style-name in a Java class, and it will bring me to the relevant part of the style in the CSS file. Same thing for Spring integration- it can connect all your code to your Spring XML config seamlessly. When you ask it "find all uses of this class/interface/member", it just does the right thing, whereas with Eclipse it often seems to miss things. Refactoring especially, in Eclipse seems to miss a lot of things that IDEA gets right.
I had the "misfortune" of having learned IDEA as my first IDE. So I am forever spoiled now. You could say that I am biased towards IDEA because it's what I learned first, and you'd probably be right to a certain extent. I tried on several occasions to migrate to Eclipse, with the intent of lowering the communication barrier between me and my colleagues. But each time I ended up going back to IDEA because it just works so much better at navigation. If you work in big codebases this becomes really important. Before IDEA I used to use Emacs and the command line exclusively.