The Annotated Edition

A version of a written text, more often than not a collection of previously released material, that contains notes from the author (or someone else with insight into the work) in footnotes or sidebars.

This is very common with textbook editions of texts using foreign languages or archaic forms of English, usually to explain idioms that would never make sense to us modern, English-speaking folk. For instance, pretty much anything Shakespeare wrote has a few annotated editions. The Canterbury Tales and Beowulf, being written in Middle and Old English respectively, are also commonly available in annotated editions.

Also common with certain classic works of Literature, especially those with a reputation for being "dense." Finnegans Wake and Ulysses by James Joyce can be nearly impenetrable without annotation.

It can also serve as a way to explain creative decisions if the creator is A) still alive and B) the one doing the annotations. This variant is very common in collections of comics.

Comic Strip Collections

 * Bloom County: The Complete Library has annotations to explain then-relevant pop-culture references and explain who the political figures being caricatured are. Breathed himself pops up from time to time to explain character origins or thought processes, but mostly just to tell us which strips he thinks are his crowning moments of funny and which are Old Shames.
 * Calvin and Hobbes's tenth anniversary best-of book has notes from Watterson, many of which go into more detail on his assorted Author Tracts or give artistic insight.
 * Pearls Before Swine's treasury collections contain annotations from Pastis which try to elaborate on where ideas came from and detail reactions to the more controversial strips. And tell us which things he found impossible to draw.
 * A few of the Dilbert collections (usually the specialized ones) also have text commentary.
 * Jess Nevins has a cottage industry annotating Alan Moore's League of Extraordinary Gentlemen. An interesting variation in that his annotations are not published WITH the books, but first on the web, and, at least for Vols. I and II, in book form separately (Heroes And Monsters and The Blazing World). Moore has said that the existence of these annotations meant that "we could be as obscure and far-reaching as we wanted".
 * Nevins has also posted annotations for Kingdom Come, Top Ten, The Nail, and other comics.

Literature Reprints

 * The Annotated Alice, an omnibus edition of Alice in Wonderland and Through the Looking Glass with annotations by Martin Gardner explaining historical context, obscure in-jokes, etc.
 * The Annotated Christmas Carol includes the original text of 1843 and Dickens' 1867 Public Reading Text, which had its world premiere in America and hadn't been reprinted in nearly a century. The notes include explanatory descriptions of foods, customs, legal terms, socio-economic references and so on.
 * The second printing of America (The Book) contains humorous "fact check" annotations in red ink.
 * The Art of War is commonly released in annotated editions, because some of the things said in it are vague, and some context is useful, and other things require some knowledge of early chinese history to make sense.
 * The Bible has a multitude of annotations. And these have annotations of their own.
 * And depending on the translation and the publisher, those annotations can be insanely biased towards a particular interpretation. The guidelines for the King James Version specifically banned anything other than cross-references and alternate glosses in an effort to keep unwanted Puritan influences from creeping in.
 * Around 1970 the Classic Publishing Corporation put out a series of classical books with annotations, such as Captains Courageous and Around The World in Eighty Days. The annotations explained the meaning of words modern readers might not understand.
 * Most good editions of The Divine Comedy are heavily annotated: at the remove of 700 years or so, and given that Dante went on Author Tracts and Author Filibusters in long stretches of the work about now-forgotten Florentine politicians or abstruse theological issues, it's often very difficult to tell who's who or what Dante is on about now without extensive footnotes.
 * Leonard Wolf's The Annotated Dracula (1975) explained a great deal of background information about the work that most readers wouldn't know about.
 * Almost all editions of Shakespeare's plays are annotated in some fashion.
 * Ian McKellan published an Annotated edition of his screenplay for the 1995 film adaptation of Richard III, and it's an invaluable look at the process of adapting Shakesepeare to the screen. It's also available for free reading on his website.
 * The Annotated Sherlock Holmes is a two volume onmibus of all of Arthur Conan Doyle's Holmes stories, in best-guess chronological order, with lots of annotations.
 * Two Gentlemen of Lebowski's first printing was an annotated edition, to keep up the pretense of it being an authentic reprint of a Shakespeare play. (To be fair, the author did such a good job keeping the linguistics authentic that a fair amount of the annotations are necessary to follow the piece.)
 * The classic long-form poem The Rime of the Ancient Mariner was reprinted twice: once with revised language and once with a "gloss" that explained several things.

Webcomic Collections

 * Bob and George has the on-site commentary, which currently goes up to March 31st, 2004.
 * The printed collections of Penny Arcade have text commentary.
 * Narbonic is a special case, in that it's available in a separate annotated edition, which came after the "vanilla" release was completed.
 * Queen of Wands did rapid-fire annotated reruns after the comic was completed.
 * In-Universe example: This Tales From the Pit comic is an annotated version of the previous comic.
 * David Willis adorns every page of his Shortpacked collections with annotations, and scatters them sporadically about the Walkyverse collections.