The Trigun fandom has adopted "Making Sandwiches" as their pet euphemism, after a scene where Milly and Wolfwood are discussing sharing Millie's freshly made lunch, then immediately following that up with a shirtless Wolfwood staring out a window, and an obviously naked Millie asleep in the background.
The inhabitants of Amazon Lily have a tendency to use the world "jewels" to refer to testicles, best seen with their interaction with Luffy. Now, thanks to Luffy, they think that men carry their family jewels (as in real jewels) in a small skin sack near their legs. Luffy, being Luffy, doesn't understand this and is natural horrified when they ask to see them
The Macross franchise features a multipurpose euphemism in "Deculture", borrowed from Zentraedi slang, originally a profanity of some kind, but by the latest entries in the series it's become human slang meaning, roughly, "awesome!" Zentraedi wishing to still use it as a profanity usually use the full phrase "Yakh deculture!"
One episode of Sailor Moon had Makoto (Sailor Jupiter) argue that she was best suited for the main role in a school play, because she had the largest breasts. When it was translated for American broadcasting, she instead claimed to have the greatest talent. However, there was no way for them to remove the rather unambiguous gesture that accompanied the line and its original meaning. Since then, SM fans enjoy using the word 'talent' and 'being talented' for... well, having large breasts.
Another unusual euphemism for Sailor Moon: Haruka (Sailor Uranus) and Michiru (Sailor Neptune) were lesbians in the original Japanese anime and manga. But in Cloverway's English dub, they became "cousins." As in Cousins who kiss.
In episode 5 of Strike Witches, the seemingly innocent protagonist Yoshika has a very... interesting dream about her best friend in the Strike Witches. Her best friend misinterprets her trying to explain her dream as 'flying in formation with her'. Yoshika is about to correct her and say "No, 'perverted misconduct'" but quickly sees the writing on the wall and substitutes "Y... yeah, 'flying in formation'. That's it exactly." The pun being that the words Yoshika used to describe it can also be heard as 'flying in formation', and it took her a second to catch on.
The title of FLCL. Throughout the series, these four (intentionally) ill-defined syllables are used throughout the series to refer to, among God only knows what, sexual acts. This has lead viewers to (falsely) believe it to be an onomatopoetic Japanese expression referring to breast fondling. In the first episode's manga page interlude, Naota's grandfather hears "furi kuri" and mistakes it for "kuri kuri," which is the actual onomotopeia for he calls it dough kneading.
In Texhnolyze the euphemism for a gang-war is Matsuri, which is Japanese for "Festival", though the offical translation calls it a "Spectacle". Its purpose is mainly to demonstrate how people in the show feel about violence as a way to solve problems.
The claiming of "Vital Regions". Made significantly worse in the show (both sub and dub) when Prussia's invasion of Silesia is referred to as an invasion of Austria's "little happy place".
To "pull a Turkey" is to hold in your pee. Don't ask.
"HAPPY END" has become a euphemism in Mirai Nikki, especially after Yuno actually got hers
Considered how Nanoha has to almost vaporize people with her magic, who later become her friends, befriended has gained a completely new meaning in the fandom. As seen on the page:
befriend (v.): to use mecha-class beam weaponry to inflict grievous bodily harm on a target in the process of proving the validity of your belief system. — From a post on rpg.net
Toradora! has Ryuuji and Minori using the ability to see ghosts as a euphemism for love. It actually makes sense; Minori is saying that's she's never seen a ghost, but she still believes in them, and she's not sure what to think when other people say they've seen one.
When Hinata Aki of Keroro Gunso finally appeared in a swimsuit, only one word could be used to describe her... assets. "Dynamite!" "bakuretsu", or "explosive", is often used in this context in Japanese, and that's a fairly good English equivalent.
In Hayate the Combat Butler, the yakuza who are initially after Hayate (after his parents sold his organs to them to pay off their gambling debts) are constantly refered to as "the Very Nice Men".
Appleseed: "It really gets on my tits that she wouldn't see us in person!"
In the series DearS, the Lady Killer of the series often asks if the woman with him would like some Coffee. How the situation is (like how the girl is getting dressed in the background) strongly suggest this is a euphemism for sex.
One episode of YuYu Hakusho had Yusuke fighting what appeared at first to be a female demon. When Kuwabara complained that Yusuke was being too rough, he explained that, in the course of the fight, he learned that his opponent was actually crossdressing. The Japanese had him put it as the demon having "something downstairs", but the dub gives us this wild variation.
Yusuke: The family jewels have not been stolen.
Tengen Toppa Gurren Lagann: When Yoko expresses her feelings for Kamina by kissing him, he reciprocates with a kiss of his own and then remarks that he'll "pay her back ten times over" after they return from their upcoming battle.
Kamina: When we return, I'll pay you back ten times over. Remember that.
Yoko: Couldn't you have put that a little more romantically?
Anime fandoms in general have "plot" as a Euphemism for "Breasts". It stems from the oft repeated phrase: "I watch anime for the plot" when face with a group or individual who holds a combination of (largely negative) anime sterotypes (Always having girls with big chests and a focus on nothing but fanservice to begin with). While it comes from these negative origins, the euphemism is heavily used by fans.
At the end of the Fullmetal Alchemist Edward Elric uses "Equivalent Exchange" in order to propose to his childhood friend Winry Rockbell. Winry even calls him dumb for using such an awkward term.