I am very verbose commenter for both other people coming behind me (in closed or open source software[1]) as well as myself a year down the road going back through thick code and needing to get back up to speed on it.
Because of this I frequently use HTML formatting in my Javadoc (lists, code snippets, etc.) and find Eclipse's Javadoc formatter more or less perfect.
It breaks lines exactly like I want it to, leaves blank lines entact where I want it to, etc.
I've attempted to file bugs for IntelliJ over the years to refine their Javadoc formatter and they have been fixed, but it still misses the boat on complex single, multi-line or Javadoc comments that requires hand-editing.
I know it's silly, I just can't get over that.
I also find the module/web/deployment/artifact model untenable; but even that I could get around if I had an effective formatter. (FWIW the Eclipse/WTP model is just as stupid when it comes to J2EE project modeling, so no one wins that battle)
[1] http://www.thebuzzmedia.com/downloads/software/imgscalr/java...