I am a new-comer to Clojure, and an intermediate user of Emacs. I have found that configuring Emacs to work well with Clojure took quite a bit of fumbling around on my part (I am pretty sure a lot had to do with my lack of understanding) but one I do have everything up and running, it usually just works.
Unfortunately my experience with DisClojure (Netbeans) left much to be desired. Its progressing slowly, but its not there yet. I haven't used Eclipse or IntelliJ so I really can't comment on those.
So what IDE among the three (Eclipse, Netbeans, IntelliJ) has the best Clojure plugin? Do you have any experience with any of them?