At my current gig we use multiple IDE’s for different tasks (of historic reasons as well as pure productive reasons). Today the team uses Borland JBuilder, Intellij IDEA and Eclipse.
The suggested/preferred choice is JBuilder, but the project has decided to be IDE independent, and today JBuilder is almost exclusively used by the EJB- developers (team is split between EJB, Web/Frontend and Persistence/Hibernate). The Hibernate Team uses Eclipse, since it makes a lot of sense to use some of the rich plugins available for this IDE.
The project has a directory structucture set up, an ant file for building/deploying etc. The problem is that JBuilder seems to spread a lot of files around the whole repository, ad hoc META-INF directories, .class files in strange places and some other arbitrary files.
I must say that I am no JBuilder fan, but it has some really nice features for those not that into “code” (i.e. WYSIWYG/Code generation for e.g. EJB’s). But I highly dislike it spreading it’s files all around it, as said before Eclipse & IDEA has no problem with a predefined directory structure, but JBuilder really insist on rolling it’s own, highly annoying. For the time being I believe I got it under control by hacking strange JBuilder xml-files, and heavy usage of .cvsignore .. I only wish it were easier.