Those lovely people at Panic software have put together a utility to batch shrink vector-based PDF files, such as those produced by Illustrator, on the fly. They use Apple's own Preview.app engine to pull all of the extra "crud" out of files that Adobe builds into PDFs made with their software:
What was all this extra crud? Will started digging into the files and brother, you won’t believe what he found. Swatches, patterns, preview bitmaps, all sort of metadata; even though we’d specifically turned off all the extra options when saving from Illustrator: Preserve Illustrator Editing Capabilities, Embed Page Thumbnails, etc.
You can download the