Todd's landlord threatening to cut him while brandishing a hammer.
When Todd is being questioned by Zimmerfield and Estevez about Patrick Spring's death, he is asked if he saw anything weird that day (he also remembers when he apparently came across himself from the future — and almost mentions it but decides not to):
Todd: Yes— no...m-maybe, I don't know...
Estevez: Are you aware you just gave every possible response to that question?
Then after Dorian is killed and Todd is arrested, he is let go after no evidence is found to convict him:
Todd: So I'm not a suspect in anything?
Zimmerfield: You're a person of interest. Permanently. Even though you're not necessarily an interesting person.
Todd: ...That feels unnecessarily rude.
The entirety of Dirk and Todd's first meeting — which has Dirk breaking into Todd's apartment.
Dirk: Oh, my name is Dirk Gently, I'm a detective. I live here now, and [reclines on Todd's couch] I'll be sleeping here tonight.
[Todd gives Dirk a look that plainly says "the HELL you are!". Cue Gilligan Cut to Todd shoving Dirk out the door and throwing his bag out after him]
After Bart chases down Ken with a machete after thinking that he is Dirk Gently, she finds out that she's got the wrong guy:
Bart: What, are you kidding right now? Then why did you run?!
Ken: You have a machete?! And you killed Red!!
Bart: Why didn't you say "I'm not Dirk Gently"?
Ken: BECAUSE I DON'T KNOW WHO THAT IS!
The introduction of the Rowdy Three:
Todd: What's going on? Dirk: The Rowdy Three! Todd: There are four of them. Dirk: I'm wildly aware!
And this from episode 1 of season 2, when Vogle and Amanda are on the run from Blackwing:
Amanda: We're the Rowdy 3.
Security guard: There's only two of you.
Amanda: SHUT UP, MATH!
The entire bridge scene during episode 2. Special mention goes to Rimmer countering a question about why he wants the dog back by asking why Dirk and Todd stole it, at which point they have to sheepishly admit they don't know.
Dirk and Todd hope to get some answers from the big bad, and discover he is as clueless about what is going on as they are.
Dirk: Aww... nuts!
In ‘Watkin’, Dirk calling Todd to come out to play
Dirk: Todd, come out! Farah says she’s solved the mystery!
Farah: (corrects him quietly)
Dirk: Todd, come out! Farah says she didn’t solve the mystery!
Fake!Agent Wheedle holding up his badge when Farah walks in, she ignores him completely and checks on Amanda, and confused, he continues showing his badge to Farah’s back. Also his random-related-word-association interrogation style: “Aiding. Abetting... Probable Cause.”
Todd and Ken's wordless exchange in the final episode as they finally cross paths: an exasperated shrug that says so much: "They're nuts, right?" "I know, right?"
Farah are the others are legally prisoners of Hobbes and Tina. If Dirk and company wanted to, they could have easily escaped or done actual harm to the two within the first five minutes. Instead, bless her, Farah goes from pointing out to Hobbes and Tina how they're supposed to be treating her and the others as prisoners to just rolling with the crazy and delighting in her good fortune at getting to do what she loves with these adorable idiots. And that's not even getting into Bart's status as prisoner...