In Court Of Roses, when Nocturne takes action to save Merlow from Dorcas, Merlows invitation echoes back at him, showing a literal interpretation of hit em at the core.
El Goonish Shive: Nanase has just come out to her ex-boyfriend and is terrified of how her mother will react. Elliot, not sure how to respond, pats her fairy avatar on the head and says "Normally I'd put my arm around you to comfort you, but I don't want to crush you." Later, after Ellen tells Nanase that she wants to be with her regardless of how hard it will be to keep it secret, she says "I'd give you a hug, but I don't want to crush-" before getting interrupted by a soapy mini-glomp.
Everyday Heroes: on the day Jane got out of prison, she told Mr. Mighty that even though she's broke, homeless, and unemployed, it's still the best day she's had in a long time. Years later, she repeats the line after telling her story to the neighbors ... and getting a hug from her daughter.
In Gunnerkrigg Court, Chapter 6, Antimony jokingly says, "I'll save you, little girl!" as she jumps out of the tree after Kat. Two chapters later, Kat repeats that line when she swoops in on her hovercraft and saves Annie's bacon. And in the flashback chapter "Ties", Mr.Thorn gives a young Eglamore some advice that shows up in one of the earliest chapters.
Homestuck does this pretty much constantly. The author even states that he's building a storytelling vocabulary so that the readers will get the idea quickly when he uses the same phrase again in a different situation. He even does it with visual gags, deliberately putting two different characters in identical poses in different parts of the story to symbolize some emotion or other plot relevance. One of the characters even runs his own webcomic, which the other characters are privy to and quote constantly as an inside joke. And then when the story cuts to a bunch of aliens, they do it all over again, copying the echoes from the humans story into the aliens story, to get the point across even more efficiently despite the fact that there is virtually no way the two groups could have known all each other's references in such a short time.
A major example occurs in the form of Belkar referring to himself as a "sexy, shoeless god of war" (after killing a pile of hobgoblins, naturally). Later, when a hallucination of Lord Shojo forces Belkar to "scream" what he IS, he actually mumbles the line in the real world, which just happened to have been misinterpreted as the response to a question by a cleric, who then healed Belkar of his sickness and, yeah, awesome ensues
Punch an' Pie has a big one when Angela runs into a friend of her ex-boyfriend's. She makes with the Self-Deprecation in trying to explain why they broke up, but the friend corrects her: his reasons were exactly the same as those of the woman who more recently broke up with Angela.
Starslip: Vanderbeam's suit costs more than Mr. Jinx's carapace wax.
In O Human Star, the first thing that Al says to Brendan when they reunite is "Are you just going to stand there?" It turns out that that's also what he said right before their first kiss.
In Modern Day Treasure Seekers, Sam uses the phrase "I'm awesome like that" to brag, but later when she's disconsolate and crying, Cade uses the phrase "We're awesome like that" to cheer her up.
Syr'Nj, in GuildedAge, tells Byron "You have a choice" when trying to calm his berserker rage to prevent him from killing any more of their team, though it doesn't work. Later, when Syr'Nj is possessed by the angry wood elf goddess, Byron repeats it back to her, and this time it works and enables Syr'Nj to toss away the magical artifact she's being possessed through.
Zebra Girl: When Sandra was attacking her friends right before her banishment, Crystal tried to calm down Sandra by appealing to their friendship. Sandra cruelly told her she knew what she was doing and that "It won't work" (and it indeed didn't). Years later, when the two of them met again, Crystal and her friends are setting up an ambush, with Crystal acting as a scout/bait. Sandra contacts Crystal telepathically, telling her once again that, whatever she is doing, "It won't work", but that she wants to make everything right again with her, as she is no longer looking for a fight, is truly repentant, and is carrying an injured Sam with her. Except this time, Crystal doesn't trust her.
At the start of Lucid Spring's prologue, Viktor, hallucinating vividly and panicking, calls Repa an "unforgiving hell forest." Toward the end of the prologue when we can see in detail what Pacem and Viktor are seeing and find that it's aptly named, Pacem shouts, "We are notDYING... IN THIS UNFORGIVING HELL FOREST!!"