Jones lampshading his Hypocritical Heartwarming treatment of Ramirez in one side-quest in Case 7, after having snapped at a suspect who insulted Ramirez for mishandling some much-needed information (which Jones himself has criticized Ramirez for previously).
Jones:(chagrined) I can't believe I just took Ramirez's defense. Oh, stop laughing, (player's name)!
Jones' reaction to the elderly Lydia Holly's crush on him during a side-quest in Case 8, where you and he have to repair and return a set of binoculars that she accidentally dropped. Your character is implied to have asked (jokingly) if Jones intends to ask her out.
Jones:(with a horrified expression) WHAT?! Of course not, I don't wanna ask her out! Come on, she's at least 130 years old! (scowling) No, that was NOT funny. Just...Never mind, let's go.
Jones' reaction, in Case 11, to your having found several critical clues in the sewers while managing to stay dry on the sewer walkways, while he himself went sewer-water-diving and found nothing.
Jones: What the...?! You're telling me that I dived into the sewers and found NOTHING, while you stay nice and dry and find all this?! Huh... (sullenly) Well, er, excellent work, (player's name)!
For a case full of Nightmare Fuel, Case 26 has some rather funny moments in it.
At the outset, you and Jones find the Necronomicon at the murder scene. Jones' reaction on witnessing the book's admittedly creepy design?
Jones: KILL IT! KILL IT WITH FIRE!
Later in the case, you and Jones get hold of one of the infamous Arkham Books, the Book of the Dead, which then proceeds to insult Jones. Yes, folks, Jones got insulted by a book.
Jones: So, what was the message hidden on the cover? ....."Screw you"!?!
Much later in the case, you and Jones happen upon a clearly sleep-deprived Ramirez.