Any conversation between Harry and Bob. Especially when Bob comes into line of sight with any attractive women.
There's also pretty much anything involving Toot-toot.
When Harry promises to promote Toot-toot to Major-General of the Guard:
If a glowing exclamation point had appeared above his head, it wouldn't have surprised me.
Whenever Harry tries to say something in Latin. Stupid Correspondence Course.
Whenever Harry knows he's about to get in trouble with sex, he uses ice water to kill the mood. The first time, he poured a cup of ice water directly onto his crotch to avert some bad decisions. The second time he managed to pour it on the woman in question and turn it into a Crowning Moment of Heartwarming in their relationship.
The end of the novella Backup, when Harry's complaining about how his latest case went to hell. Thomas, who actually knows what happened and was partially responsible for said case going to hell, somehow manages to keep a straight face.
Harry: You know, Thomas, sometimes I feel completely unappreciated. Thomas: Wow. What's it like?
Less from actually knowing and causing the case to go to hell and more being told his little brother feels unappreciated when he just disguised himself as hammy villain, took a rather painful blow from said brother and killed the true villain before she hurts Harry, all in order to protect him from harm and possibly deadly knowledge.
From "The Warrior":
Uriel: You're... you're trying to bill the Lord God Almighty? Harry: Hel— uh, heck no. I'm billing you.
Harry is trying to deal with two werewolves with psychic parasites flirting with/attacking him and Molly keeps distracting him by yelling alarming questions from the lab about fire extinguishers and acid while smoke billows out.
Anastasia walks in while Harry is trying to give CPR to Molly—who is topless at the time—and Harry starts stammering that it is NOTwhat it looks like. She looks around and laughs, before saying she has no clue what this looks like and simply must know how it happened.
"But it's my day off!" - Which doubles as a shout out to Clerks.
From "Something Borrowed," when Harry makes it clear he's not going to be talked down to and insulted by Billy's stepmother-in-law:
"Though you obviously aren't Georgia's mother. Howsabout I call you trophy wife? (...) Bed warmer? Mistress made good? Mid-life crisis byproduct? When in doubt, go with the classics. Gold digger."
He grunted in Martian. Fuck off and die. It's an expressive language, Martian.
A minor bit, when Murphy goes to visit John Marcone. After Murphy correctly deduces that the person that suggested she talk to Marcone is actually one of his informants, Hendricks looks at Gard, who gives him an annoyed look before passing him a $20 bill. The fact that they were betting on whether or not Murphy would figure it out just made this troper laugh his ass off for some reason.
In "Last Call", Harry tests a doorknob, "just in case," and is disappointed to find he doesn't have to bust the door down.
And the Parody Magic Spell he uses to scare a thug into revealing what he knows: "Intimidatus Dorkus Maximus!"
Pretty much all of Gentleman Johnnie Marcone's narration in Even Hand, due to the man being an absolute Deadpan Snarker. However, there are a few highlights:
Marcone's reaction to being told, essentially, to shut up or else:
Is it so much to ask for civility?
Not to mention the sly references to Hendricks being much smarter than he looks, the suggestion that someone who works for a vampire should have "a bit more fortitude"...Marcone is just a fountain of CMoAs and CMoFs.
From "I Was a Teenage Bigfoot", we get Harry commenting on how Dr. Fabio could have named the school "St. Mark's Academy for the Resourceful and Talented", thus making the acronym "SMART" instead of "SMAGT". And then proceeds to use the word to trash Fabio's shrine.
In Bombshells, Molly's prayer to God when faced with a Wire Dilemma.
''...but if you could just do me this one solid, it would be really awesome for a lot of people."
Even some of those. For example, there's a section dealing with the idea that having Harry around could potentially interfere with storylines, and that in that case it might be easier to run the game if you kill him off in the background, with a list of ways this could have happened. Harry, naturally, is not amused, and his comments on the subject◊ are likely to induce slightly nervous, uncomfortable giggling. Crowning Moment of Mood Whiplash?
But especially "Someone needs to explain to this guy that if you simultaneously carry a katana and wear a trenchcoat, you're a dork..." Hah. Take THATSephiroth!
It's probably a reference to cliche World of Darkness and Shadowrun characters, especially given how said vampire is mentioned in relation to a game of Evernight.
It's also a callback of sorts; the first time Harry met Sanya, he was wearing an overcoat, and wields a saber. It would be pretty easy to mistake it for a trenchcoat-katana combo.
Or when Harry complains that if "Jim B." is his player in real life, he needs to roll better.
And in the start of the second book, when it credits Jim Butcher as the author, Harry has a minor freak out and asks who the hell this guy thinks he is.
"Do not fight Happy Fun Merlin. Back away slowly."
Hell, the files for pretty much every powerful entity. Among other things, Billy leads off the notes on Nicodemus with "You lose.", lists the Erlking's Refresh Rate as "Ha!", and laughs at the idea of writing up definite stats for Satan.
Harry complaining about the capricious dick of a GM he's got.
I demand 23 retroactive Fate points.
"I hate when you reduce my insecurities to game mechanics."
Harry swearing he would needle Peabody about his grammatically incorrect German, and following through in the novels.
One section concerning the Knights of the Cross and other people who use their Faith for power has a handful of passages blacked out entirely by Dresden, with the note that Billy should take them out because some people may not like them speculating on the nature of the big guy. If you copy and paste these lines, you find they are, in fact, Jim Butcher breaking character to tell you he's not going to open that can of worms just yet.
Harry starts to notice that a lot of the illustrations (based on events from the book) involve half-naked villainesses attacking him, and wonders what this says about him. Bob approves of the pictures with some enthusiasm.
During Arturo, the porn director's profile, Bob starts pestering Harry about getting him some videos for "research." later on, in Lara's profile, near where it mentions she acted in porn, Bob starts asking Harry again why he never picked up the videos.
In the description for "wolfweres", animals that can transform into humans:
Harry, Billy, and Bob have awesome banter throughout both books. At one point, the text refers to "keep it simple, silly."
Bob: Isn't it "Keep it simple, stupid?" Billy: Georgia... encouraged me not to address the reader as "stupid." Bob: Did she encourage you in the sack? Harry: Aaaaaaand you're done.
Bob's opinions on what Skills scores Harry should have.
Bob: (Regarding Burglary) William, Harry should have a decent score in this. Harry: Shut up, Bob. — Bob: (Regarding Deceit) Harry should have a low score in this. Harry: Shut UP, Bob. — Bob: (Regarding Intimidation) Also a skill for creepy PI wizards. Harry:Bob! Shut up!
Another index entry with a surprising amount of listed pages? "Jerks". Lampshaded after Harry calls yet another person a jerk.
Harry: Rudy's a jerk. Bob: You keep saying that about people. Harry: Well, I've met a lot of jerks.
One picture of Murphy facepalming has Harry commenting, "I make her do this way too much."
Harry's Comments on Mouse (in the Temple Dog section)
As much as I complain about my Dogasaurus Rex, I'm glad Mouse stowed away in the Beetle. He's saved my life a bunch of times. And all he asks for in return is a little kibble Okay, a lot of kibble. Fine, a HUUUUGE amount of kibble.
At one point when the text says "Life can't be all puppies and rainbows," Harry highlights it and margin-notes, "Why not?"
On the page detailing the Supernatural Sense power, Harry's sidenote mentions that there's a guy in Pennsylvania who can see through drywall. JUST drywall.