Continuing the discussion from Where do you put your reading notes?:
I've been with LiquidText since the first beta, and have admired how it has evolved -- with increasing polish and features attentive to how users actually work. As a PDF annotation tool, I don't think it can be beat. There is a bit of a downside in getting notes and comments out of the app. Export is all-or-nothing -- and only exports to PDF, DOCX, or the LiquidText custom document format. I prefer my notes separated into individual documents or nodes in an OPML outline. If someone doesn't need that, then LiquidText is fine. I'd mention that the absence of Mac version is no problem now that we have Universal Clipboard and apps such as Copied. It's easy to put all of one's notes on the clipboard on an iPad and then open Tinderbox on the desktop and paste (and perhaps explode) the notes.
MarginNote is sort of like LiquidText but maybe the overlap is more in the order of 50% or so. As I mentioned in the other thread, I love MarginNote's ability to quickly consolidate multiple documents into a single "notebook". If I have 5 or 10 related documents in the same topical notebook, I can easily make an outline or mind map in MarginNote and link together clippings / notes / images / scribbles from across all those documents into one mind map.
MarginNote is also better for research -- text in a document can be selected and a browser opened to find additional web content related to that text. MarginNote has a much broader set of features than LiquidText -- and many more options for exporting notes. Including sync with MarginNote desktop. It is also a bit rougher around the edges -- the UI is unusual and sometimes confusing. MN syncs via iCloud -- WebDAV is coming soon they tell me -- but to sync notebooks you have to make sure there is at least one annotation added to the notebook. Took me ages to figure out that's why documents I captured on iOS never showed up on the Mac.
So, I use LiquidText when I want to just focus on a single document. (Yes, I know documents can be linked / containerized -- I just don't use it that way.) And MarginNotes when researching taking notes on a topic involving numerous documents and web content.
There's no bright line separating the two apps. If I had to choose to delete one or the other, I would delete LiquidText. Both developers are super nice and responsive.