I used Together (version 2) daily, for about two years… I've moved away from it some months ago, but now with arrival of version 3 I've just had a look back, and checked the new version out. I think Together is a fine app with good, mac-like design and great support. While development of new features isn't very quick, it gets constantly improved and there are frequent bug fixing updates. The upgrade to version 3 I find somewhat underwhelming – iCloud syncing is nice, but overall it feels more like just a face-lift of version 2; nothing substantially new for me.
Together is a very versatile app – there are so many things you can use it for and different ways to actually use it, that I find it rather difficult to do Together justice in a review. For me, it was all about managing my ever growing documents library I need for doing research (about 8000 files, mostly PDF but some other file types as well, like pictures, sound, video, etc.). I did take some notes in Together, but that wasn't its main use for me. Anyway, I liked this app because with it I was able to sort my files for each project in groups and attach comments, tags and labels to each file, save searches in smart folders and so on. Very practical, and while one gets many of these features already with the mac's Finder, it is nice to have all work-related files separated from all the other files on the mac. And, of course, Together offers nice features like the bookmarklets for Safari (or any other browser), organising groups and smart groups into folders, etc.
However, having to deal with a large documents library, Together wasn't the right app for me. For example, I wished to be able to define the author(s) or editor(s) of a document and then browse my files by author, by editor, etc. In Together you could only kind of do that with the comments field (not comfortable) or with tags and tag bundles: make a tag bundle for "author", another one for "editor", etc. But well, if a person is the author of one document and the editor of another, you run into problems, because the tag can be only in one bundle. So you end up with rather simple tag bundles, like just "people" instead of "authors", "editors" etc. And then the process of tagging is quite cumbersome in Together if you want (or need) to do it systematically, because there is no help apart from auto-completition; you will easily forget one or another tag bundle, and then you have many files with incomplete tags. Another annoyance with tag bundles: sorting by drag and drop is pain if you have many tags – scroll and scroll and scroll through the sidebar…
Regarding price, personally, I can see a 20$ price tag for Together, as it is now on sale at the MacAppStore. But 40$ is too much with this feature set. For just ten bucks more you can get an unlimited license of Sente. Sente is a documents managing and bibliography citation app. Even if you don't need the citation features, the documents- and file-management is worth it, Sente feels like Together on steroids. Here you can specify custom document types (with custom fields) – so for example, if you have some video files, you can define what information should be attached, like "year", "place", "camera type", "author(s)", "editor(s)", etc. etc. whatever you like. This makes entering meta-info so much easier and it's great for finding stuff, because when creating smart groups, you can define more precisely what files you want to see. And well, if you like tags and tag bundles, these are just so much better done in Sente: you have hierarchical tags and a quick tag entry panel, where you can just click which predefined tag applies to the file – this speeds things up dramatically and it's so much more comfortable to use, you'd never want to go back to Together's tag bundles. If you have two different versions of the same document, you can save the two (or more) files at the same reference entry. Very useful. Oh yes and in Sente's PDF viewer you can annotate your PDFs, highlight text and so on – if you are just on the go, you can also do that on your iPad, since you sync all your documents (or the Libraries you want) through the cloud, because well, it's 2013 now and as a mac user you can expect an app to have a useful iDevice companion (in case of Sente, it's even free).
Anyway, this is not to say that Together is bad – other users may find an app like Sente (or Papers, BibDesk, etc.) bloated and complicated and they'll gladly pay extra for Together's ease of use. However I recommend to assess what you need the app *exactly* for before investing money and (more importantly:) time in it. For managing a large documents library I can't recommend Together.