* EnsembleDarkhorse: Some of the most popular characters in the series have less than a third, or even a fifth, as many scenes as Lemony the narrator does.
** Lemony's friends/associates all have their fans, particularly plucky aspiring journalist Moxie Mallahan, Cleo Knight (the CoolCar-driving DamselOutOfDistress who hopes to save the town with her chemical invention) and the taxi-driving Bellerophon brothers.
** Dashiell Qwerty is beloved by the fanbase of being a helpful, cooly designed authority figure providing a welcome exception to the franchise's use of AdultsAreUseless.
** Prosper Lost for some, due to being a rare adult who, while not necessarily helpful, isn't a complete idiot or unreasonable either.
* MagnificentBastard: [[spoiler:[[BigBad Hangfire]], true name Armstrong Feint, is the chairman of the [[AnimalWrongsGroup Inhumane Society]] and mastermind of a plan to destroy the town of Stain'd-by-the-Sea and its inhabitants. Once a kindly zoologist, Hangfire became livid with the town's policymakers when they made a series of ill-advised decisions that killed countless local animals for little real benefit. Beginning his revenge spree by murdering an old Colonel who had the town's oldest tree torn down to build a statue of himself, Hangfire stays one step ahead of the heroes at all times as he dismantles Stain'd-by-the-Sea's infrastructure piece by piece, taking actions such as burning down the town's only school to force its children to transfer to a fake school run by him, kidnapping the heiress to its largest business, subverting the town's last remaining medical staff and police officers to protect him, and manipulating his own daughter, Ellington Feint, to bring him a statue of the [[SeaMonster Bombinating Beast]], which would give him the ability control to the real Beasts to have them devour the town's children, avenging his beloved animals by giving the town a traumatic reminder of what really matters.]]
* MoralEventHorizon:
** Hangfire does a lot of awful things, but probably worst single thing we hear about is [[spoiler: letting Ellington think he was kidnapped so she'd go along with his evil plans.]]
** Stew crosses it when he [[spoiler: murders Qwerty]].
* ShipsThatPassInTheNight: Ellington Feint/Moxie Mallahan is awfully popular, probably because of the BettyAndVeronica aspect of it, even though Moxie hates Ellington in the story and Ellington has almost no interactions with Moxie.
* TheyWastedAPerfectlyGoodPlot: There are fans who'd hoped//wanted Hangfire and the Inhumane Society to tie in with Olaf and the V.F.D. Schism.
* TransAudienceInterpretation: Some interpret this exchange between Lemony and Ellington from ''When Did You See Her Last?'' to hint at Lemony being a transgender boy. The use of AmbiguousSyntax means that Ellington could be talking about dressing up as a boy or the plan the two are about to enact.
-->'''Ellington''': What do you think, Mr. Snicket? Do I look like a boy?\\
'''Lemony''': No. From a distance, maybe.\\
'''Ellington''': How is this going to work?\\
'''Lemony''': It's easy. I learned how to do it.\\
'''Ellington''': From your organization.\\
'''Lemony''': Yes.
* TheWoobie:
** Just about all of the kids Snicket befriends, trying to eke out a living in a DyingTown, with several of their parents having died or abandoned them, and who end up being exposed to more than one murder by the end, which takes a toll on them.
** Among the adults there's Prosper Lost, who is gradually revealed to be deeply mourning his wife (who died in a fire which also destroyed much of his once majestic hotel) while having to keep up a pleasant facade for his customers. He also experiences a lot of parental worries about his daughter, who he doesn't see as much as he'd like due to having her live with her uncles (the town firefighters) to keep her safer from fire danger.