These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Adaptation Displacement: To the point where Gerritsen's latest books have "Rizzoli and Isles: Book title here" instead of just the title itself. Also, note that there is no separate section for tropes in the main page that belong solely to the novels, unlike the page for Dexter.
Complete Monster: Charles Hoyt was Jane Rizzoli's Arch-Enemy, a necrophiliacSerial Killer known as the Surgeon. Preferring to target couples and loving to foster fear in his victims, Hoyt would rape his female victims, forcing the male to watch, then kill them both. Hoyt managed to kill three couples as well as an entire family. Forming an obsession with Jane, Hoyt murdered Alexander Ghent and kidnapped his wife to lure Jane into a trap to kill them both. He uses his scalpels to leave permanent scars on Jane’s hands. Though captured, Hoyt continued to be a menace through his apprentices. Hoyt would go on to temporarily break out of jail and murder one couple with his first apprentice, threaten to rape Maura Isles when she interviewed him while he was in custody, murdered the husband of his second apprentice, had his second apprentice take Jane's brother, Franke, hostage, and used his third apprentice to kill an inmate to lure Jane to him so he could have one last attempt at killing her before he died of pancreatic cancer. Just before his final attempt on Jane's life, he began to slit Maura's throat just so Jane could watch her best friend die before killing her.
Crosses the Line Twice: In the second episode, an old lady insults the aged detective who comes by to ask about her son, due to their history together. Then she calls Rizzoli a "greaseball dyke cop". Then she uses a sardonic tone when addressing the black Frost as one of those "Affirmative-Action cops. Which island did you come from? Do you speak English?" This all happens in the space of about two minutes. Oh, and she's clearly Irish.
Die for Our Ship: To the point where any man put in the way is ruthlessly run over. Casey is a prime target of this.
Genius Bonus: Whenever the Boston skyline is depicted, the weather beacon on top of the Old Hancock Building will match whatever weather might be shown in the following scenes. (It'll blink or shine steadily in either red or blue; the color patterns and their meanings are well known to Boston residents.)
Harsher in Hindsight: Season 1 episode "Born to Run" has Jane and Maura competing in the Boston Marathon and getting caught up in a case where two runners are shot dead in the middle of the race. Two years after the episode aired, the Boston Marathon was the target of a terrorist attack that killed 3 people.
Jerk Sue: Jane in the books. She's brusque, abrasive, has such an irrational dislike of beautiful women that she spends most of the first book treating a rape victim like crap and is pathologically defensive regarding sexism. But somehow, she received such positive feedback that Gerritsen nixed plans to kill her off and instead kicked off a still-going series of books with her as the lead character (or one of them).
Just Here for Godzilla: Some fans of Rizzoli & Isles may be attracted to the show because they are fans of Angie Harmon and Sasha Alexander from their old shows. Based on the ratings, it may now be a case of Come for the X, Stay for the Y (in this case, come for Harmon and Alexander, stay for the quality of the show).
Les Yay: Consciously played Up to Eleven by the producers (who are very aware of their lesbian fanbase) and the actors, even though Word of God is that Maura's and Jane's relationship is and will remain platonic.
There is a series of "Subtext Recaps" on afterellen.com where each episode is analyzed under the assumption that Jane and Maura are closeted lovers, and that their various male love affairs are just attempts to keep up appearances. Not surpisingly, the recaps spend about twice as much time on the Les Yay than on the actual murder cases.
Moral Event Horizon: A variation. Paddy Doyle was a ruthless mobster who had standards (no women or children on his hitlist). However, as "Dance with the Devil" reveals, he was personally responsible for the death of Cavanaugh's wife and kid, effectively breaking his personal code of conduct.