Now that I am writing on a computer instead of an iPad, I want to reiterate the value of DevonThink Pro Office. This is probably the best app that was never developed for Windows, the app I wished for in so many ways, for a long time. I collect a lot of information, word files, web pages, pdfs, photos, etc... DT is a database program that lets you create a file structure to organize materials. You create groups, and put info into them. You can tag files for sorting; DT has a very powerful AI that will help searching through large repositories. And to look for commonalities among files. It has the ability to bring into the database ANY TYPE of file that can be read on a Mac, and if QuickLook can view the file, so can DT. You have full search tools inside of it, AND everything is indexed by spotlight.
It has the ability to convert PDFs to text-readable files (the program comes with a high end OCR scanner); it can import email messages. It has a Web Clipper that will take a page and turn it into a paginated PDF, this alone is remarkable. The PDF is an exact replica of the web page, but split into 8 1/2 by 11 pages. I use it daily.
All files in DT are copies of the original, so the original file you bring in is untouched, but the database package is a complete container. I successfully store each database in a dropbox folder and am able to use them on multiple machines (I just try to make sure the database is not open on both, so I don't have version-control issues).
I have used the tagging features as a way to do a basic content analysis of materials; I use DT to manage my courses. And I can sync materials from it to my iPad. Without a doubt DT is my favorite mac program, and it has changed the way I work.
An example of a research database. Cases I am using. I convert moist text into RTF (from within DT), and sometimes even do my writing in the RTF editor it provides, although this example shows a text-readable PDF. DT handles PDFs very well.
Here is one of the same database, but showing tags, I have highlighted one tag, and only the files that meet that set show up, you can "command-click" to select multiple tags.
Here are two of my personal library "Mike's Library" - notice it can bring in RSS feeds.
This one shows you how you can get creative with it -- I have a series of maps of downtown Chicago with details as RTF files tied to screen shots from google maps, and I keep them on the iPad for convenience. I can also sync them to my iPhone.
Here is an example of a course database, in which I mixed text and PDF screen shots of readings into my class notes.
Yes, I am sold on this program, and try to evangelize for it. If you have a mac, you should consider one of the versions of DT, but Pro Office is so worth it. I think it is $149, I paid a little less for the education pricing. There is an app store version for $49, but it does not have the OCR-capabilities.