M&M is an obvious example; there are many (Tolstoy, Dumas, Conrad, Zola, Proust and, in more modern times, Patrick O'Brian) where historical, biographical and technical annotations would be hugely useful and fun. In the case of translations, concurrent access to the original would also be awesome.
One of the earliest web versions of this that impressed me was a "Web 1.0" hypertext version of T. S. Eliot's The Wasteland, which is a poem constructed almost entirely out of allusions, and which makes little sense without the necessary annotations.
Do any of the eBook formats support anything like this? Have anyone done this in a way that's accessible in any meaningful way on a Kindle?
Heavily annotated books pre-date the Internet - my edition of M&M footnotes and endnotes the hell out of the book for context.
There is also an active Bulgakov facebook page [2] with things like fan art and informations about upcoming adaptations.
As a matter of disclosure, I created the facebook page in 2008, but it has been run for many years now by Jan Vanhellemont, the man who is also responsible for [1]. I consider him to be the foremost fan of Master and Margarita on the English language internet.
[1] http://www.masterandmargarita.eu/en/ [2] https://www.facebook.com/m.a.bulgakov/