There's a very nice app called Jalopy that can do bulk pretty-printing according to a very customizable set of rules, including the Sun ones. It can be run stand-alone from the command line or as a plug-in to Eclipse (and IntelliJ, for that matter).
However, I believe that if you right (menu) click in the Explorer view on the directory that contains the Java files of interest, select Source/Format, all of the Java files in that directory and its children will be run through the formatter. I do recommend making a backup first, though.
An IDE is no substitute for an Intelligent Developer.
Before using the "Source->Format" option, you need to be sure that it is set-up as you want it to be, and maybe you need to run the "Source->Clean Up..." options first - and then maybe you also want to perform a "Save Actions" each time you save your code....