I’ve been struggling with this issue all my life, and if you don’t want to use a web-based solution, I suggest you download WordCleaner from the idiotically named “Zapadoo” corporation (http://www.zapadoo.com/).
This program is quite neat, customizable, and it lets you batch-convert from right within Word.
Sometimes you’re going to have to deal with .doc files, and the easiest way to throw it online while keeping the sweet, sweet formatting (you know, italics, em-dashes, crap like that) is to run this proggy. It’s free for 15 days, then you apparently gotta pay.