The storyarc title "The Good Prince" is pretty much universally understood to refer to Flycatcher's rise from janitor to king, and all the sacrifices, ordeals and wondrous feats he had to endure and achieve to get there are the main focus of the narrative. But one must also consider Prince Charming's journey during this arc as well. As Mayor he successfully thwarts Imperial envoy Hansel, sets up a spy network of zephyrs that prove crucial to Fabletown's clandestine information gathering, unifies Fabletown's biggest, most important figures at the most crucial, yet dividing time in the history of their society, and lays the groundwork for their greatest, most important undertaking: the invasion of the Homelands. He truly starts to come into his own as a leader and a Prince, and has begun to shed the more irresponsible, short-sighted and selfish aspects of his character, becoming the truly heroic and inspiring Prince he always should have been. Charming is indeed the other "Good Prince".
Towards the end of the war against the Empire, an Imperial general leading the assault on Fabletown's Fort Bravo orders the retrieval of a magic arrow from his quarters. It has been overlaid with powerful spells that will enable it to pierce any magical defense, en route to its selected target, "the enemy's foremost leader and battle champion", and slay said target. The arrow is fired, but Boy Blue, wearing the heretofore invincible Witching Cloak, sees the arrow coming and attempts to shield Bigby, its supposed target, from its impact. But the arrow merely passes right through Blue's cloaked arm to continue on its deadly path to Bigby's shoulder, knocking both fighters out. What's key here is that if what was related to us about the power of the arrow is to be taken as true, Bigby, the intended target, should have died from the piercing, even though it was in a non vital part of his body. But it is tragically Boy Blue who later perishes, albeit slowly. From this it can be conjectured that the arrow's enchantment, despite the Imperial general's assessment and intention, designated Blue as the most vital and potentially dangerous member of the enemy camp, as he possessed not only the Witching Cloak (enabling him to transport virtually unlimited amounts of personnel, ammunition, weapons, rations and other supplies) instantaneously, but also the Vorpal Sword, a blade capable of cutting through nearly any magical defense and killing anything.
The short "In a Castle Dark", from the "Farewell" collection isn't just referring to Castle Dark. The title is another goodbye from the author; it's part of the lyrics to the Gordon Lightfoot song, "If You Could Read My Mind". Full lyrics here.
It might initially seem strange that characters from Land of Oz are counted as Fables, but L. Frank Baum intended for the series to be a "modern fairy tale", so it only makes sense that they'd count.
And you won't read that book again, because the ending's just too hard to take...