YUI Compressor does both JavaScript and CSS. I'm not sure if you can send it a batch of files.
You can batch process at YUI Compressor Online (yui.2clics.net), though that version only accepts JavaScript. Another Online YUI Compressor (refresh-sf.com) accepts CSS, too, but doesn't batch.
In terms of comparing the various minifiers, see jQuery : Frequently Asked Questions (FAQ) : How do I compress my code? Also, check out Microsoft Ajax Minifier.
jQuery has switched from the YUI Compressor to Google's Closure Compiler for the minified version that they distribute.