[I'm labeling this as a "comment" rather than a review since I'm covering several apps.]
Okay friends, based on some addition info in another thread [http://tinyurl.com/7axh7j5], I've decided to create a new database in DevonThink Professional Office.
While I knew DTPO was powerful and easy to find data, I didn't realize how awesome it is also WRT importing files and folders. I had previously set up a bunch of nested Finder folders where I dropped some 4000 assorted files (URLs, web archives, text files, PDFs, images, scans, and a few others) onto the new database. It took barely a minute to import all these files, which were contained in some 300 folders. All the folders remained intact and are now "groups" under the main library. Using the quick search field I looked for instances of "bento" to see what I had. In an instant these files popped up and I was able to browse them. DTPO's browser allows one to view the files at once without having to rely on Preview or Word to open them.
Since I'm already fairly familiar with DTPO and I have a Fujitsu Scansnap scanner (that DTPO recommends), it now seems to be the logical choice.
Once I did this, I figured I'd try importing into both Together and iDocument. Together wouldn't let me import my entire stack of nested folder but rather one group at a time. Even though Together lets you index files rather than directly import them into its own database, I was not able to do this when importing folders. Also, Together burped on a few files and crashed on me. Searching on "bento" was as fast as DTPO and the PDF showed up in Together's own window without having to rely on Preview.
With iDocument I was able to import my entire stack of nested folders and their files in one operation. No burps. However I don't like the viewing choices in the main window (icons, icons in groups, very ugly and space-wasting lists). Searching on "bento" was a breeze but here to look at a document, whether a text file or PDF, Together requires you to view in Text Edit, Word, or Preview, which isn't exactly what I'd call integrated.