I use bookends, and it is great for this. it has a notes category and i keep many of my notes in that, much the same way that you mention. But bookends is mac only. http://www.sonnysoftware.com/ . I am happy to trade endnote xml files produced from bookends with other people’s files if they have them available. The search tool of bookends is quite amazingly adept, it has both regex and sql capacities. Bookends also plugs into word and other word processors, such as the one that I use, which is Mellel at http://www.redlers.com/ . I also have just started using copywrite to write too, because it has the option of full screen mode writing http://www.bartastechnologies.com/ . Bookends works fine with copywrite.
Alternatively you can use my online reference tool. http://referencetool.tmttlt.com/ The more people that use it, the faster I will probably upgrade it’s capacities. The referencetool that is online now is mainly just wikindx3, but It does precisely what you seem to want. I’ve been working on a parallel project for some time now that might be released in the fall that does the same thing, only differently, but it will be data compatible with wikindx3 , so no one will lose any data.
The other thing that I use, but not really for references, but for quote and paper/pdf management is devonthink. Steven Johnson shows how he uses it at http://www.stevenberlinjohnson.com/movabletype/archives/000230.html
I use it differently. I download or print every document to pdf that i deem appropriate, currently around 11000 different pdfs, I make sure that they are all full text pdfs, and then devonthink makes them searchable. Devonthink is basically what i chose to replace any Desktop Search tool, such as apple’s native spotlight, which failed miserably on full text phrase search in pdfs.
so.. I have another step in process, in comparison to yours, which is to put almost everything into devonthink as a whole. Then I put the citations and specific notes into bookends, and I occasionally export my bookends database to wikindx3/referencetool.
bookends + referenceminer http://www.sonnysoftware.com/
Hope that helps
Alternatives to Endnote and CiteULike?:
I’ve just posted a question about useful alternatives to research citation manager tools such as Endnote or CiteULike to the AoIR mailing-list, and I thought I’d repeat it here as well. My approach to research is to store key quotations from a source alongside the bibliographic reference, but none of the standard tools I have come across seem to do this particularly effectively (e.g. in Endnote, the best available workaround appears to be to create an additional field for quotes in the bibliographic record, but this is clunky and doesn’t work very well with multiple quotes stored against the same record).