ALANTERRA  I just wanted to put in a short review saying how much I like PDFPen. If you are considering Acrobat Pro, definitely check out PDFPen--it might be better and cheaper for your purposes.

I first bought PDFPen for "light editing" of PDFs. Even though I own Acrobat Pro 8, I wanted a program that was specifically meant for editing pdf documents. You know when you have a form that has spaces that you are supposed to fill out--like with an IBM Selectric typewriter--PDFPen does that perfectly. It also assembles PDFs out of a group of separate documents, so you can take the form, delete the 3 pages of instructions, add the essay answer, paste in your signature and date, and just email back the final application without scanning or printing.

But, I just figured out today that the other thing PDFPen does well is that it "understands" multi-column documents. If you have ever tried to select text in a two-column document using Preview, you know what a PITA it can be. But PDFPen understands the document better, so you can select just the text you want.

I also use PDFPen to highlight passages in documents, just like reading a real paper document with a yellow highlighter in your hand!

I haven't tried the OCR yet, but have read that it is as reliable (or unreliable) as Acrobat's. I'll compare the two programs later.

But, in general, there is little that most of us need to do with a PDF that PDFPen can't do.

A

Oh, PS, I don't think it has ever crashed on me. I'm not sure I can say that about any other program I use (maybe BBEdit, not sure).  
(Version 4.0.4)

ALANTERRA  This is just a short review. I looked at Papers and decided to not use it.

Its user interface is well-thought-out, but it feels very incomplete. I could not figure out how to add a book or a book chapter as a reference type (and neither could a number of other people who posted to the forums). There isn't a manual that you can search for answers to simple questions, only some introductory movies plus forums on the developer's site. I ran into a number of refresh problems, which, until you figure out that they are just cosmetic bugs, cause pointless head scratching (do I not understand? is the program broken?).

As a way of browsing lots of pdfs, and for looking up bibliographic data in Google Scholar, this program is awesome. But if you move beyond its strengths, you find it hard to know how to continue.

I would definitely look at this program and see if it meets your needs, but also check out the alternatives, from Zotero to Sente (ie, from free to much more expensive).

A  
(Version 1.8.6)

ALANTERRA  I haven't explored all the features of Sente, but it seems to be head and shoulders above its competition. I spent the last few days looking at Sente, Papers, Zotero, and one programs that I didn't even bother to look at due to bad reviews (EndNote).

For my needs, Sente is the best. I am trying to organize a couple of thousand pdfs (and a few other kinds of documents), and continue to research various areas from that base. Sente seems to have a strong emphasis on medical research (it uses PubMed as a default database to look for things, and I haven't figured out how to change that). But the tools of being able to look up bibliographic data automatically in Google Scholar, use keywords, and browse pdfs from within the program make the program exactly what I need.

As of Feb 2009, the developers are giving some insight into the next version of the program, which looks to be a useful improvement. It will be a free upgrade to anyone who purchases the program after Jan 1, 2009.  
(Version 5.7.3)