Various, including 'mokkori' for anything related to sex.
A story arc used "going to pee" for "exacting righteous revenge on a Yakuza clan that burned down a park just to Kick the Dog and believed they'd get away with it thanks to the lack of evidence". Ryo was one of those who used it, and his revenge had a level of epicness proportional to his Gag Penis.
Code Geass fans adopted the term "Lulu Quality" as a euphemism for "being the universe's punching bag", following an interview where the show's staff insisted that they really are fond of Lelouch, they just do horrible things to him because they want him to learn a lesson and become a better person.
In 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.
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.
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.
"HAPPY END" has become a euphemism in Mirai Nikki, especially after Yuno actually got hers
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".
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
The Macross franchise features a multipurpose euphemism in "Deculture", borrowed from Zentraedi slang; originally a profanity of some kind, by the later entries in the series it's become human-influenced slang meaning, roughly, "awesome!" Zentraedi wishing to still use it as a profanity usually use the full phrase "Yakh deculture!"
In One Piece, the inhabitants of Amazon Lily hadn't had any contact with men prior to the arrival of Luffy. When he's asked about what that thing he has between his legs is, he answers that it's his family jewelsnote The Japanese version used the term "Kintama" which is slang for testicles, which the amazons took to mean "Kin Tama" which means "gold balls"., causing the amazons to believe that all men have actual jewels hidden between their legs. Luffy, being Luffy, doesn't explain the misunderstanding and is naturally horrified when they ask to see them.
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 faced 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.
Also, to specify a bit more: It's always "plot" with the quotation marks as the euphemism. Without them it's actually referring to the plot.
Another unusual euphemism for Sailor Moon: Haruka (Sailor Uranus) and Michiru (Sailor Neptune) were lesbians in the original Japanese anime and manga (and in the upcoming Viz Media dub). But in Cloverway's English dub, they became "cousins." As in Cousins who kiss.
When Hinata Aki of Sgt. Frog 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.
Shimoneta: During the infamous "cookie scene," Anna explains why she calls her vaginal fluid her "love nectar." It's because it begins to build up inside her as her feelingsfor Tanukichi intensify, 'til it finally discharges whenever she experiences orgasm.
So, I Can't Play H!: In episode 1, Ryosuke tries to see Lisara's panties when she steps out of the bath. So he shoves his face under the shirt she's wearing and plants himself flush against her nether region. Except she wasn't wearing anything underneath it, so he ends up getting a faceful of her "red threads" (i.e. her pubic hair)!
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.
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: *laughs* Kamina: Wh-What? Yoko: Couldn't you have put that a little more romantically?
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.
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.
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.
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 a demon in drag. The Japanese had him put it as the demon being "hooked up underneath", but the dub gives us this wild variation.