Support for exporting annotations in readers is terrible. None of the companies really support it. And how good what is out there is depends on what you want to do with the exported annotations.
The Kobo devices possibly have the best support because of the Annotations plugin and Kobo Utilities (both my plugins, but I inherited the former from someone else). Which is better depends on what you want to do. I believe that @Quoth prefers the Kobo Utilities because he uses the annotations for proofreading books. Once he has fixed the source, he discards the annotations. If you are keeping the annotations as favourite quotes or something like that, the Annotations plugin might be better as it adds the annotations to the calibre library. There are several other ways to get the annotations from Kobo devices that are discussed in the Kobo forum.
Kindles are probably the next best as there are several ways to parse the "My Clippings.txt" file. Including the Annotations plugin. And I think Amazon has a page to display the annotations for books in their cloud. Kindles save the annotations somewhere better than the "My Clippings.txt", but, I haven't seen mention of a tool that reads this.
The other devices I now anything about are the tolino and Sony's. The tolino is similar to the Kindle. The "notes.txt" has the annotations without real location info. They must also be stored elsewhere, but, this is not accessible. Sony's are no longer available, but I recently added support for them to the Annotations plugin. This was based on someone else's work, but, I haven't heard if it works.
The Annotations plugin supports getting annotations from Kobo, Kindle, tolino and (hopefully) Sony ereaders. Plus the Goodreader app. Support for other devices or apps can be added.
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