As I alluded to before, here's a bookmarklet that will append the current date and time to the end of any URL before sending it to Yahoo's My Web, allowing you to create a dated cache of any page without overwriting your previously stored version: MW-date
Obviously this breaks the social aspect of the bookmarking tool, as no-one else will bookmark that exact URL, so you'll probably still want to use the standard bookmarklet most of the time.
Another problem with this, in an academic context, is that many pages will be behind subscription barriers, so Yahoo's spider won't be able to get in to archive them. Greasemonkey or a Firefox extension could be a solution to this, but I'm not sure how yet. Does anyone know how to download a file (a PDF, say) to a temporary folder, then upload it somewhere else (eg to an upload form), from within a Firefox extension?