Ulysses III has recently had an important update. It now assigns and reads OS X tags. This brings the Ulysses’ value for academics to an entire new level. Ulysses III has already been great for taking project notes (e.g. on teaching or publications) because it can organize its sheets by hierarchical folders corresponding to work areas and projects. However, Ulysses lacked good capacity to effectively manage reference notes, which may be used for several projects including those that don’t yet exist and are more logically organized by tags or keywords.
Before the latest update, Ulysses’ native keywords could only be assigned to its own internal notes and used only from within the application. However, academics often need system-wide tags working accross multiple file types: pdf-documents, plain text notes, presentations, emails, etc. That’s why there is a premium on system-wide tagging systems such as OpenMeta which is now merged into OSX Mavericks tags. That’s why I was so disappointed with Papers3 which complicated assigning system-wide tags to scienfitic articles.
The latest version of Ulysses allows assigning tags to notes that are stored outside of its library. For example, all my NValt notes are stored as plain text files in a folder called “Notes”. Ulysses reads from this folder as an ‘external source’ so I can also see all my NValt notes in Ulysses (in addition to Ulysses own notes). Now Ulysses allows to assign OS X tags to such notes so that I can find them from outside the application (e.g. through Spotlight).
A couple of improvements can still be made. Most notably, the tags assigned in NValt appear in Ulysses with considerable delay. Moreover, it has not been clear to me how to easily search for a tag or a keyword in Ulysses (except by creating a smart folder).
Tags in a sheet from an External Source in Ulysses III
The same tags assigned in Ulysses III are searchable through Spotlight
Academic workflows on a Mac 
My main reasons for buying Ulysses were that it has a very nice way of organizing documents (as you have detailed previously) and that it has a good companion iOS app with which it can sync via iCloud. That finally stopped me waiting for an iOS companion to Scrivener.
This OS X tagging capability sounds great, but I’m at a total loss as to how to assign tags to a sheet or stack in Ulysses (as opposed to viewing tags previously assigned elsewhere).
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I think I have an answer to my own question. Since I prioritize synching with Daedalus, most of the files I have in Ulysses are from Daedalus (i.e. in the Daedalus section in the sidebar). Looking at the few files I have in the On My Mac section (mainly the usage guide files), I notice that there’s an Attach command at the top right that allows adding keywords. I assume those are written to OS X tags. Unfortunately, however, that Attach command does not appear in the Daedalus section. I suspect there’s no way round this limitation, though it would be wonderful if someone had a good idea.
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I’m glad you’ve figured it out. Maybe in iOS 8 they will have some sort of tagging feature and it will sync with tags from Macs.
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That would certainly be nice!
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