I initially kept my list of papers (mostly academic) organized in http://delicious.com/ as a set of links and in bibtex so that I can refer to them. But this approach has many shortcomings, not the least of which is the difficulty of maintaining it. I then switched over to using a personal Mediawiki instance to manage it: this has the benefit of storing the paper and any meta-data about it. But this is also slightly painful to maintain.
Mendeley is excellent: I use it to manage a collection of several hundred PDFs. Favorite features include its automatic renaming of files, in-line highlighting and note-taking, automatic lookup of paper metadata via Google Scholar, and great support for OpenOffice, Word, and BibTex. Its search capability is also very good. And, it's well-integrated with the Mendeley website, where you can make a collection of papers a public folder to share with colleagues. Finally, it's cross-platform, which is vital to me as a Linux user.
I have not used any of those. Have you looked into http://www.Evernote.com? I don't know if it will do what you want but it will allow you to save and index many documents. It even OCRs text.
So for example you can take a picture of a menu or a specimen and upload it and it will automatically OCR whatever text is in the image. You can then search for words in the image and they will be returned. It will also return results for any documents that contain the word you search for.
Papers is great, although I think the (upcoming?) next version will include a lot of features that makes it more of a topic-agnostic research article organizer. One thing that it (and Zotero) do that Evernote doesn't is pull in bibliographic information automatically, and then allows you to search/sort based on metadata fields.
I know this area very well, Evernote is not the answer. The three examples that you've listed: Papers, Zotero and Mendeley are much more appropriate. My tool of choice is Papers on the Mac and I use Dropbox for online access and back-up.
Some other options that you haven't mentioned are: