* CrazyAwesome - Jack and Jeronimo walk a fine line between sanity and insanity and are really awesome because of it.
** Technically, both of the are ''literally'' insane, the former has tertiary neurosyphilis (later cured, but who knows what damage it has already done) and the latter has Tourette's Syndrome.
* EpilepticTrees - Tons of them involving the Solomonic Gold and the true nature of [[spoiler:Enoch the Red]].
* FridgeBrilliance:
** [[spoiler:''Literature/{{Cryptonomicon}}'''s Rudy von Hacklheber, brilliant mathematician and cryptographer, turns out to be descended not from Lothar von Hacklheber, alchemist banker, but from brilliant French mathematician and cryptographer Bonaventure Rossignol, as well as the brilliant Eliza De La Zeur.]]
** It seems at first glance that Daniel, an atheist Natural Philosopher and courtier, is quite unlike his anti-Royal Puritan father, Drake. But, in being a major player in the change from Royalty to the new System of the World, he turns out to be his father's son.
* NightmareFuel - Daniel's kidney stone operation and the story of how Jack became "Half-Cocked". The descriptions of the effects of smallpox and the attention paid to 17th/18th-century sanitation (or the lack thereof) probably count as well.
** In-story, Hooke and Wilkins's experiments at Epsom provide Daniel with this.