zenrain wrote: Currently when I do this I separate out the attachments into individual thoughts and make the note applicable to the attachment.
Yes that's an option, but that implies to cluter space with redundant thoughts that deal with exactly same issue.
Regarding your other input:
Having a reference managment system for attachments would bring Thebrain to whole new level as a research tool. And sources could have their own specific database so that when the same source (URL, Pdf, etc.) shows up in different Thoughts you won't have to fill the reference fields twice.
If you think about it, you could even reference specific bookmarks inside a pdf so that you don't just open the pdf as a whole but go to a specif spot inside it. Thebrain could thus take over in research field, where DOCEAR http://www.docear.org (unfortunately discontinued) was doing a great job.