Hey Deb, thanks - like I said earlier, we'll put a UI on the search prefixes soon so you don't have to type them by hand.
Surfergirl - thank you! We haven't added Mobipocket.com yet, and for the other stores the issue is crawl frequency (these sites do not give us access to their datafeed). Our infrastructure is limited at the moment, so we can't crawl Amazon and BoB more frequently, leading to a slightly outdated index for these sites. As Inkmesh matures, we will invest more resources in crawling these sites more frequently, and you will see fewer discrepancies.
Steve - yes, we definitely want to include indie authors and smaller sites; I will email you to follow up.
Ahi - that's a good idea. We already crawl different websites at different rates, but we need to spend some more time figuring out the best way to discover and index smaller websites.
wallcraft - it is interesting that you mention the need for a standard catalog format, because an effort to create one is already under way:
http://code.google.com/p/openpub/wiki/OPDS. It is still in draft status, and I suspect it will be difficult to get sites like Amazon to adopt it, but it could become a very useful feature for small to mid-size websites. FeedBooks and The Internet Archive are active participants in OPDS discussion.