What good academic research management software is there?

Could it also display the articles and allow note taking on them directly, plus generate reports that include those notes and page numbers? Zotero's note field is almost completely useless.

interesting. I've never heard of such things before, playing with mendeley now.

It doesn't do everything you want, but I've been using Papers for a few years now. I've used Mendeley and Zotero before, but I think that Papers is a slightly better product.

It's not free, however.

I've recently started playing around with new software [Qiqqa] (http://www.qiqqa.com/62832) for this purpose. The core of Qiqqa's nice features are:

1. OCR /text extract everything. Since everything is OCR'd, you get some decent auto generated title author.
2. Streamlined metadata retrieval thats human powered- just click a button, it takes you to an inline google scholar page where you click the correct "import bibtex link" and then it intercepts that bibtex and does the rest for you.
3. Robust tagging system.
4. Some sort of reference tree where you can see what cited what in your library. WARNING: I haven't tried this, my library isn't yet extensive enough to do this. Also some sort of generic brainstorming/mindmapping tool. I have yet to figure this stuff out.
5. The completely optional ability to sync libraries (of which you can have multiple) on the web between computers or share them with friends for a price that is measured in total MB of upload/download as opposed to $x per month, and which seems to be pretty cheap.
6. A very responsive development team so far- the default screen shows a list of new features added month by month and thanks the users individually by name who came up with the ideas. Maybe I just like this because my name appeared.

Not sure what else. It won't immediately find the references for an article but it may streamline your ability to grab and organize a growing stream of references. Please suggest your idea to the developers as well. Shameless plug: If you use this referral code to make an account on their website [http://www.qiqqa.com/Register/62832] (http://www.qiqqa.com/Register/62832) me and you both get some free time with their pro features. I am more interested in seeing the program succeed and develop more useful features than saving money though, because right now it is just not quite good enough.

sorry, i can't help, but great softwares. wow.

I agree that searching by bibliography reference would be a fantastic tool, as would in-text highlighting+notes. Also, it would be very nice to be able to hyperlink to specific places in the literature, i.e. you could put a link in a note that would take you to a contradictory passage in another report. Another important aspect of research is data. I think Wolfram has some good ideas with their new document format, if we had a zotero-type application that would pull relevant numbers from a collection of papers, that would be fantastic. It would also seem that the CDF would let you pull equations/methodology, but that might be asking too much.

I think part of the problem is the PDF standard itself. In order to implement these things effectively, you'd probably need to write an entire PDF editor on top of your organizational software.