Complete Monster: Culverton Smith is shown to be even more of a monster than he was in the Canon, and is even mentally labeled this by Holmes. Smith goes around infecting people with his deadly tropical diseases just to study the results, then murders hisstep-nephew out of Greed for his stepbrother's estate (an action on which Moriartyactually calls him out). Then he gloats over a dying Sherlock Holmes, and this rewrite of a canonical scene is actually pretty painful to read. All this makes his eventual fateimmensely satisfying.
Like You Would Really Do It: Some fans said this when Holmes disappeared for several chapters and was believed dead - however, the reaction was hardly apathetic. During the fact, the reaction was desperate; after the fact, it was relieved. Apparently, quite a few readers were genuinely scared for Holmes.
OTP: Lestrade/Annie. To the surprise of the author, Annie Lestrade quickly became a popular character, and one reviewer even referred to Geoffrey and Annie's marriage as an OTP.
The Woobie: Pick any page of the FFN reviews, and you'll find loads of sympathy (and sometimes even tears) for Sherlock most of all, Watson secondly, and Mycroft thirdly. Lestrade and Wiggins get honorable mentions for having almost as much angst as Mycroft.