One of the great things about the internet is its ability to enable collaboration--workflows are never static, each of us builds on the work of others to enhance our own productivity. After my last post, Writing Workflows: Capturing Annotations to Enhance Scientific Writing and Knowledge Retrieval, I received a boat-load of comments, suggestions, and links. Thanks!I suggest you take a look at an entry in Aleh Cherp's excellent Macademic blog. In a recent entry, a guest author discussed limitations with the built-in annotation tools of Papers, Sente, and Mendelay. His preference for annotating manuscripts is the open-source Skim. I've been playing with Skim recently (especially some of the post-annotation processing tools). I used Skim in the past, but curtailed my use in order to simplify my workflow (doing everything within Papers2). Despite the rich annotation tools in Skim, I set it aside because of the extra steps needed to make Skim highlights visible in Papers (and visa versa).As pointed out in the comments section of my last entry, the Achilles Heel of my annotation workflow is the need to separate my highlights / notes file by hand (Papers puts out a single aggregate file with all highlights and notes batched together). Although there are scripts available to send Papers2 notes to DevonThink Pro, I could never get them to work properly. I'm experimenting with a modification to my previous workflow--one that will significantly speed up the process:

I highlight and make notes in Papers2 on my Mac or iPad as I discussed in my last entry.
When I've finished annotating, I make sure the most current version of the paper is synchronized back to my Mac. I then "Export PDF File and Media" from the File Menu in Papers2 and save to a convenient location (I use my Desktop).
I then open the document saved to the Desktop in Skim and choose "Convert Notes" from the File Menu in Skim (this results in all the embedded notes being converted to Skim Notes).
I open and select the "Inbox" of my Literature Database in Devonthink (this is the location the script will save my comments).
With Skim still open, I run the following SKIM PDF Notes to DEVONthink script I downloaded here.
I return to my Inbox in Devonthink where I now have individual RTFs for each highlight or note.
I insert my own comments (if I have any) in each RTF file and save each file. I ignore the link the script generates.
If I have a comment I plan to cut and paste directly into a future project, I append my comment with the Papers Citation Index.
In DevonThink, I highlight then drag and drop all the RTFs (but not the duplicate PDF of the paper) to the "Supplemental" Tab of the manuscript in Papers (this copies each RTF into the Paper folder hierarchy).
Finally, in Devonthink, I Index (the first time) or Update the Index (all subsequent times) - NOT IMPORT - the folder.

The SKIM PDF Notes to DEVONthink script saves me quite a bit of time--I no longer have to parse my comments by hand. Happy writing!