Antidote is a UI in development for the ANT build tool, and has support for Javadoc tasks. It can also be used to run any other Javadoc doclet, such as JDiff (http://www.jdiff.org) which tells you about the differences between two versions of an API.
~Matt
The antidote README is at
http://cvs.apache.org/viewcvs/~checkout~/jakarta-ant-antidote/README?rev=1.1&content-type=text/plain
I find a standalone commercial tool just as a GUI for JavaDoc unlikely, since it is really just one command. Also, you want to run the same command again each time the code changes, so using a batch file is the best plan. Remember that batch files can call other batch files.
I have a standard JavaDoc batch file which includes my preferences and standard header / footer information. For each set of packages, I then have other files which call that file and pass in the specifics for those packages.