First one that comes to mind is Kazuma's deadpan response to his name being called in Konosuba.
"Kazuma Kazuma!"
"Yes, i'm Kazuma."
Apparently that was completely adlib'd by the actor too, it was never in the light novel. The voice acting in Konosuba almost singlehandedly carries it, it's genuinely hilarious.
Dreiko said:
"Daga, otoko da!"/"But she's a man!" - Steins;Gate
Always died laughing when that line comes up. Honorable mention to "omae wa mou shindeiru" "you're already dead" from hokuto no ken, as that catchphrase perfectly captures the story.
The one that gets me in Steins Gate is how Rintaro insists on saying Phonewave (Name Subject to Change) instead of just Phonewave every single time. The way he speaks to nobody on his phone is great too. The humour in that game is just top tier in general.
I really need to finish Steins Gate actually. I got Suzuha's ending because i'm a fucking dumbass who didn't understand the whole phone mechanic. I'm shouting at the screen for Rintaro to use the time machine and i'm just being a scrub spamming the advance dialogue button when you need to bring up the phone and put the command in yourself.
Then there's the fact that pretty much every female character (all the plot relevant ones anyway) in BlazBlue feels the need to address Terumi by his full name, at least as an opening line if not all the time. It's not funny or anything, it just pops out to me. It's not even just an English dub localisation thing, the original dub does the same. All the males just call him Terumi and it's not even just a villain thing since Izanami does it too and she's (kind of) on his team.
*Terumi walks in*
*gasp* "Yuuki Terumi..."
Every time. Guess it's a dramatic effect thing since he's likely come to fuck up your day since even if he's Meme Tier gameplay wise he's top tier in the canon.