Somewhat disturbing example: in The League of Extraordinary Gentlemen volume 2, when Mina Murray learns that Hyde has taken care of the Invisible Man, he is quick to assure her that "I attended to his end. Rest assured, it was... comfortable." Being a proper Victorian lady, Mina takes comfort in this assurance of a painless death, not twigging for a second that this actually means that Hyde brutally sodomized the Invisible Man before beating him to death.
In The Sandman, a caption describes devil-turned-nightclub-owner Lucifer playing a medley of unreleased (fictional) Cole Porter songs that Porter only performed privately for friends, ending with "She Never Went Down on the Titanic." (Someone really needs to write the lyrics to that.)
A storyline in Cable & Deadpool involved Deadpool's friend Weasel joining HYDRA under the very inspired name Penetrator (or, rather, Penetraitor). Predictably, this caused some choice dialogue.
Henchman 1: It seems... I don't know... provocative. Henchman 2: In almost a... gratuitous fashion. Penetrator:What? We're going to use the Penetrator to penetrate the warm, comfortable walls of mother Earth! This machine will ram home our agenda! All will know HYDRA has thrust themselves into the very womb of civilization! What's gratuitous about that...?
Wolverine: ... so I can show the Penetrator here something long and hard — and cold and sharp! Penetrator: Okay, I deserve the silly entendre, since I chose this name, but I really think you don't understand—
Deadpool: The Penetrator is my friend... Okay, wait, lemme try that again... Weasel is my friend — and he happens to be sheathed in a protective coating that allows him to safely penetrate things... Okay, wait, lemme try that again— Wolverine: Shut up!
Earlier during the run, when Deadpool attacked the Great Lakes Champions, he made fun of Mr. Immortal for owning the X-Men card set, Mr. Immortal replying they were only for flipping.
Deadpool: Yeah, I'd like to flip Kitty Pryde. Squirrel Girl: Shut your evil, evil pie hole!
A conversation during Deadpool's fight against Taskmaster:
Deadpool: Scared the pants out of me... Well, not literally, 'cause then you'd be all distracted by my two bazookas. You know — on account of I got one real bazooka — and the other bazooka would be a metaphor for— Taskmaster: Shut up! I get it. You think it was deep or something? Like your humour requires footnotes?
Also, while fighting Rhino:
Deadpool: Me am horny. Okay, that was too obvious even for me.
"Finbarr Saunders and his Double Entendres" is a strip in Viz in which the title character laughs at various Double Entendre-sounding phrases exchanged between his mother and his neighbour. It always culminates in him realising it's all perfectly innocent, only for the last Double Entendre to actually have the sexual meaning and the strip to end with his mother and the neighbour shagging.
Kara Zor-El: I'm looking through it. It's amazing. All the equipment I'm seeing. So many sizes and shapes... Linda Danvers: All the ...? Kara! Just where are you looking?! Kara: The equipment room, where they keep all the sporting stuff, why? Linda: Oh, I thought you were peeping in at the guy's lock— Forget it. My own dirty mind.
Shockingly enough, a fairly G-rated newspaper comic Pickles got a double entendre through once; the wife is tired of waiting for her husband to unclog the sink and the husband replies he'll get to it in a "sec". The wife grows furious and states "I spent half of my time waiting for secs! I don't want to hear any more about secs!" Her husband is then laughing very hard for obvious reasons and the wife is clueless as to why he is laughing. While her use of "secs" was something innocent, the husband saw that in an obviously different light.
Ditto for Moon Mullins, in which Emmy Schmaltz keeps trying to get young Kayo to turn off the TV and get to work on his homework. Kayo (repeatedly): "Just a sec, Emmy!" — which results in an exasperated: "No, Kayo! No more 'secs!'" — much to the surprise of Lord Plushbottom (speaking of double entendres) in the next room.
Catwoman: Well? Or do I have to purr in your ear? Batman: No... but maybe later you could scratch my back. Catwoman: What's the matter? No itches in the front?
The newspaper comic Cathy once featured the line than an off panel character was "in the restroom, giving the copier repairman a swirlie." The artist, Cathy Guisewite, was stunned that many readers thought that was a reference to oral sex, because she had always heard a "swirlie" was dunking someone's head in a toilet and flushing.
In a JLA Classified storyline where the Supervillain Blackguard is moving in next door. His real name is Richard Hurtz. But he prefers to be called Dick.
Spider-Man: Anybody ever point out that you're a purple-headed invader, or has Stan Lee been laughing to himself for the last forty years? Kang: Eh, you know Stan.
From Birds of Prey #103: Huntress and Judo Master commenting on Big Barda's choice of weapon.
Huntress: Looks like she pulled out her mega rod. Judo Master: It's quite a devastating mega rod. Huntress: Her massive mega rod looms large in her hand.
Nico from Runaways is a witch whose powers come from a big staff that gets absorbed into her body when she's not using it. In one issue, she fights a thug carrying a crowbar. Their dialogue goes like this:
Wrecker: Sister, you just earned yourself a taste of the big stick. Nico: Bet mine's bigger than yours.
Knight & Squire, Paul Cornell's DC Comics miniseries about British superheroes, features a pair of villains called Double Entendre, who speak in these.
"I swear, if tonight doesn't get more exciting, I'll go to the top of Big Ben and toss myself off."
When Bullseye asks Daken which side he is on as the Dark Avengers and Dark X-Men quarrel, Daken responds that he always did like playing for both teams.
One arc of New Avengers was a "Fantastic Voyage" Plot. When Ant-Man and Doctor Strange go into Luke Cage's body to retrieve an explosive device from his heart, Spider-Man can't resist reminding Luke that "you have two men inside you right now."