Anyobe of you using DTPO as a complete replacement for Finder? If not complete, what kind of files do you keep in Finder? Keen to know because I am planning an overhaul of my filesystem, it is beginning to be real messy.
No offense meant, but if your file organization outside DEVONthink is “real messy”, why would it be better inside DEVONthink? 
DEVONthink has some major strengths, but interaction with modern features of the OS X file system (the real one) such as iCloud, Dropbox & Box and their cousins, Time Machine, etc., is lacking in my opinion. I also prefer to have multiple special purpose tools that follow the one-thing-well philosophy, rather than complex mega-tools like DT.
I am spending more time planning to get data out of DEVONthink and depending on it less not more. I don’t regret the investment in creating databases, but in hindsight I would never do that again. I would rather see technology such as DEVONsphere Express and DEVONagent get really powerful upgrades – than invest more time in technology that seems to be over the hump of its life curve. DE and DA provide the best of DT’s capability. I think in a year or so that will be enough for me and I will seriously consider putting paid to DT.
But back to my first comment. INMO, It is more important to understand your data and use thoughtful heuristics and simple techniques to arrange, work with and manage it, than fiddling with complicated software.
Just my 2 cents.
DEVONthink isn’t intended to be a Finder replacement, and thinking of it in that way would, I think, hinder its most fruitful uses.
I don’t put all the files on my computers into DEVONthink databases. Instead, my collections of documents in DEVONthink databases are selected for their importance and relevance to my needs, such as collections of references and notes for research and writing, or collections of financially important items to help me track them, schedule bill payments and document tax-related items.
DEVONthink integrates the textual information content of a wide variety of filetypes, allowing one to search across them and (in most cases) see text content without having to jump around among a number of applications. The DEVONthink environment for organizing, searching and analyzing the information content of documents is much richer than the combination of the Finder (including Spotlight) and individual applications. For example, the Classify assistant can help determine one or more appropriate group locations for new content, especially when groups are topically organized. The ability to replicate a document in multiple locations without creating duplicates or adding to storage requirements cannot be done in the same way in the Finder, as replication is not the same as creating an alias of a file in the Finder.
The See Also assistant can help explore similarities among documents in a database, and so can be a great tool for exploring variations among concepts, for example. Humans are not “wired” to instantly compare the contextual relationships in a selected document to those of tens of thousands of other documents in a database. Of course, DEVONthink doesn’t “know” anything about disciplines such as chemistry, astronomy or medicine; it’s the responsibility of the human user to decide whether See Also suggestions are useful, or not. I reject many such suggestions. But quite often they stimulate thought, and once in a while create a Eureka! moment when one is lead to a new line of thought. (When I’m using See Also, I usually open promising suggestions in a new tab, using a contextual menu option to do that.)
The DEVONthink environment is a large one, and so may seem daunting at first. There are tools of many kinds, including assistants, scripts, templates, tags and so on. For example, if one selects a single word and presses the Option key at the same time, a sidebar pops out that displays a list of all other documents in the database that contain that term. Neat!
I encourage new users to start out by thinking about the collections of information on their computer, and how DEVONthink could be useful in working with them.
A user of DEVONthink Personal, limited to one main database, should think in terms of groups to collect related documents. Users of DEVONthink Pro and Pro Office should also consider creating individual databases to focus on a special interest or need. In that case, one can treat multiple databases like information Lego blocks, which can be opened and closed as needed.
Start small, and experiment! I have a friend who is very intelligent, but who is constitutionally unable to use a computer to do anything. That’s because he tries to completely understand how everything works, before trying to use an application such as Mail or Safari, let alone using his printer. He’s read all the manuals and Help files. He has had many questions for Apple support and his printer manufacturer. But he has never dived in and tried to start small, so he cannot use his computer. Instead of becoming a useful tool, his computer has become a source of endless frustration, so it’s hidden in a desk drawer. 
Thanks for all the replies.
sjk: Thanks for the link!
Korm: As I understand, the database in DTPO in not proprietary in the sense that the file is stored as it is, no changes to file/filename are made. For backup purposes, I guess TmeMachine also backs up the DTPO databases. Regarding cloud services, I only tend to use this for highly selected files, so I don´t find DTPO as an obstacle for cloud computing.
Bill Deville: Insightful comments. I share your experience in “see also” and “classify” functionality of DTPO. I have stored and worked with approximately 25% of my documents in DTPO which was previously stored in Finder. I find working through DTPO an ease compared to the Finder due to better search, tagging and the mentioned functionality not applicable in Finder. Less messy as well compared to the 75% outside DTPO. So instead of moving the rest of my documents, maybe I should move 25% more and see how that works.
Yes no changes are made to your documents, unless in DEVONthink you edit them or change their names. There are recent threads here about Time Machine that I suggest reading – yes TM will back up your databases. Nothing beats a periodic full backup – use File > Export > Archive. Never store databases in Dropbox.