Eclipse PDT has this handy built-in Yui Compressor in the context menu for files. But when building a webapp that uses multiple such files,
You can also batch-minify using Node.js. However, this option is only for Linux users (for now).
Every time some software package is horribly lacking a convenience (Eclipse) or a builder batch format is just crazy (ANT), someone clever comes along and creates something awesome.
In this case,
which is awesome.
Just thought I'd update this question and add the answer.