partly 
I understand where you are coming from but I have to say that my work has rapidly moved to modified pdf files. I am using Papyrus hybrid files for everything that I write and I am using skim to annotate the pdf files I get from everyone else.
I use DT Pro to tie it all together into a single comprehensible unit.
I’ll admit Skim is new and changing all the time but it is also an amazingly valuable tool in my daily work. It went from nowhere to critically important practically overnight. It has changed the way I work and done so for the better.
From my point of view there is nothing you could do to DT Pro that is more important than the ability to use the modified pdf files that Skim creates. It is that important.
Requested feature number 2, more file formats, includes the recognition of skim files, right? Adding chat logs and such is as valuable for my workflow as as a custom plugin architecture for adult content. Seriously, what is the point of introducing OCR and scansnap support if DT shies away from what is likely the most popular and useful (and free) pdf app on the market?
Again: The Skim file format is, at first, proprietary. So, we’d need to write special support for it. But, to add as many file formats as possible we will go for a more gneralized approach here if the Gods of Apple allow looks up, sighs
Eaglefiler, Bookends, Sente and many other developers have resolved this issue already (including single-person developers!). “Again”, the absence of substantial development by DT is explained by referring to the ever elusive veporware.
here’s my workaround until we can see our skim notes (or switch): After annotating a pdf in Skim, add a label in DT, so that you can see where you have skim notes attached. Labels can also be searched.
I’ll just chime in to confirm that, like others have stated, Skim has become a more central part of my workflow than DT. I would prefer to keep using the strengths of both, but I’m not going to bend-over-backwards to get them to try to talk to each other (e.g. writing elaborate import-export scripts to get my notes into DT).
Count me as another voice wanting Skim integration. A question regarding this — would/could quicklook provide the bridge for this? If skim files are ‘quicklookable’ (I think this is planned) couldn’t DT use the quicklook image of Skimmed PDFs?
Ditto for Mellel files
This is exactly what we’re looking for. We want to use QuickLook for reading and displaying so that DEVONthink can handle all files that come with proper QuickLook support.
Ahhh. Good stuff. I’m pretty sure this is in the works for Skimmed PDF’s and hopefully for Mellel as well.
But another question this raises - if they are available for quicklook viewing and thus DT viewing, that doesn’t necessarily mean they are indexed, right? Would spotlight importing be used in that case?
It would be a nuisance if in the future my Mellel files were viewable in DT but not actually indexed.
Everything that can be indexed using standard (!) methods will be indexed. This is what we’re working on right at this very moment.
good news… now we just have to start another thread on the skim feature request page and also generate 2800+ views on the thread… 
when I did a google search on Skim and quicklook I stumbled on to a thread that made it sound like it was imminent, but perhaps I misread it.
Skim provides a spotlight importer and a command-line tool (described here: skim-app.sourceforge.net/wiki/in … _with_Skim ). You could use the command-line tool to attempt to extract notes from a pdf, and if they exist, index the notes. Seems straightforward.
To keep stirring this pot… A while back Danzac and then Eric referred to Quicklook as a possible way forward for DT to be able to read pdf annotations and notes made in the pdf reader Skim. I shared this over on the Skim forum at the time and it was made clear this was not an adequate way forward. The Skim developers have just attempted to reach out to other apps like DT so I will paste the following over from the Skim forum. I am so disappointed because DT was the backbone to my PhD but over the last year I’ve rarely opened DT once a month because I cannot do without annotating - the notes I’ve added to my pdfs (Skim) have become my most important resource. As I write up each chapter I pull another batch of files out of DT. I hope the suggestions below may prove helpful - though they’ll come too late to help me: my computer desktop is a sight to behold!
Michael
From the Skim forum:
A new release of the SkimNotes framework and skimnotes tool is
available for download. This release contains bug fixes for reading
notes from PDF bundles. The framework and tool can be useful for third
party developers interested in accessing Skim notes in other
applications. The built products and source code can be downloadded
from the Skim home page at http://skim-app.sourceforge.net.
The Skim development team
I also use skim together with DT for my dissertation, but I keep all files in the database. My intermediate solution is different: I changed the symbols in DT (with right-click on the menu bar), so that the button for “open externally” is visible all the time. I also changed skim to be the default app for pdf viewing in OSX. With this setup, it is possible to quickly access skim annotations, while still benefiting from see also search in DT, which is still better than spotlight. I would much prefer to see my annotations directly in DT, but I’d still prefer this workaround to the crapped-over desktop…
Thanks Maak for your sharing your way of using Skim and DT. I followed your advice and have cleared my desktop as a result. I’m grateful!
In fairness too, whilst DT may be blind to Skim notes written on a pdf, it does handle the files very well. I wanted to make sure I could easily get my Skim-annotated pdfs out of DT. In dragging one of these pdf’s out of DT I thought I’d lose the notes or have to go hunting for them and then need to re-attach them to the pdf, which would be tedious in the extreme. Not so, the file drags out of DT just fine so when I drag and save such a pdf - to my desktop say - it’s a Skim (pdf file plus Skim notes file).
Skim is clearly very important to many users of DT – and I think it’s important for the DT developers to note that people who are at the bleeding edge of productivity in their fields – graduate students writing dissertations and young faculty/post-docs – are expressing a great deal of unhappiness at not having search support for their Skim bundles…
From the Skim wiki
“SkimNotes Framework
…
If you want to be able to easily read Skim notes from a Cocoa application, you can also include the SkimNotes framework. This framework provides some general API that make it easy to read and write Skim notes. It allows you to simply load a PDFDocument with any attached Skim notes included. It support Skim notes stored in Extended Attributes, in PDF bundles, and in .skim files. The framework is also used by Skim, and is included in the Skim bundle starting from Skim version 1.1.5. The framework and source for the framework can be downloaded from the Skim project page.”
Things sure have changed since I was in grad school, then. In my experience, grad students and young faculty are often at the leading edge of their fields, but rarely at the leading edge of productive work practices.
Katherine
It’d be doable rather quickly, I’d think, if DEVONtechnologies granted my deepest wish and provided an open plugin API. It’d be a matter of days, if that. And no extra coding on their part aside from opening up the API they already have and writing some simple documents and saying the whole mess is unsupported.
They’re pretty close-mouthed about the idea, though, and what few posts I’ve seen mentioning any sort of extensibility have dismissed it out of hand.
I hoped that, since all files are stored outside the database in DTP2, that they’d be more open to the idea… but nothing has been said. So I’m not entirely sure why, but it looks like people who want an extensible DEVONthink have a lot of bitching or switching ahead of them 
starts screwing around with F-Script