For those users who rely on Spotlight search results are an important part of their workflow, I can suggest a few workarounds.
I'm personally sympathetic to the Spotlight desire, at least to a certain extent. In an example of my workflow: I keep notes, draft documents, multimedia resources, and bibliographic entries all on the same artist. When I begin drafting a paper, say on the artist "Exempli Gratia," sometimes I think "hey, what do I have on her?" I then use Spotlight, and I get some conference notes, a mention in a set of lecture slides, a quicktime movie, some email correspondence with her etc. - but, of course, no citations of her writings or of other works that discuss her.
Obviously, I can simply search twice - once in Spotlight, once in Bookends. If you want to get better Spotlight results, however, I can suggest two workarounds:
Hack 1. Name all Bookends attachments with major citation information.
This will only work for entries that *have* attachments, of course, and then is only really necessary for those such as image-only PDFs, images, and multimedia files - html and PDFs with full text should already come up without prompting. Still, I give all my attachments abbreviated bibliographic titles (Name, Title, Source, Date) when I add them, and this makes Spotlight results significantly more useful to read - Finder views too:
If you keep your attachments organized by Bookends, then any filed attachment coming up in search results will remind you that there is a corresponding citation entry.
I do this not because it is helpful in Spotlight, but because it is also useful in Finder, in email attachments, in burned CDs, etc. etc. etc. [One dream Bookends feature I wish for is that I could control the default attachment naming behavior of Bookends to do this more seamlessly, rather than manually expanding the default name-date every time.]
Hack 2. Periodically export a raw text file list of authors and of titles from Bookends.
Title the file "In Bookends.txt." All it should contain is a raw list of author names and a raw list of title names, or whatever. Any time the "In Bookends.txt" file pops up in Spotlight, it will remind you that you (probably) have information in Bookends as well, and you can then search there. If it doesn't, you (probably) don't. [Note: I don't actually do this, as my attachments almost always lead me back to the individual reference.]
Hack 3. Add an attachment every time
This is a lot of work, but it would in essence be a way of manually doing what Jon doesn't want Bookends to do automatically - handle individual files for *everything*. Every time you add an entry that you want Spotlight searchable, copy the citation out of your tray into a text file and attach it to the entry, auto-renaming it and importing it into the references folder. Bam! File-based Spotlight index of Bookends. Still, major drawbacks include - double-clicking on one of these files wouldn't actually launch Bookends and take you to the citation - attachments could get out of sync any time you edited the main entry - etc. [Note: I certainly don't do this!]
Hope this was helpful.