HNNNG!Explanation Hisao's heart condition is a frequent joke with the fans as they give him random heart attacks in fan works. Later on, it escaped into the wild, and came to be used to describe any sufficiently cute thing causing a heart attack in the viewer.
After a large number of commenters spammed the above in response to one too many cute pictures, several moderators said that anyone commenting with "a certain onomatopoeia" would be banned. This, of course, led to several comments of "A CERTAIN ONOMATOPOEIA!"
"Gimme the chocolate, Hisao!" Explanation A fancomic originating on 4Chan that shows a member's initial thoughts and such, until he literally falls in love with Hanako. Then the game throws in a XXX coprophilia sex scene.
"Why does she need glasses if she's deaf?" Explanation A comment regarding Shizune from the same fancomic.
Became an Ascended Meme in the full version when Rin actually does this in her route (the first pic, that is).
"The problem is in your pants".
On the on-site image gallery, all anonymous users have the name Shiina "Misha" Mikado. It has thus become common for users to call out Misha for saying something stupid/irrelevant/etc, followed by "Wait, I'm Misha." This is a reference to her Third-Person Person tendencies when translating for Shizune.
MANLY PICNIC! Explanation (Spoilers) The bad ending of the game where Kenji and Hisao have a "manly picnic" together on the rooftop while the festival resumes.
"Anal."Explanation (Spoilers) Emi calls Hisao out to a shed, supposedly to get some gloves. Once there, she reveals that she doesn't wear any, and Hisao discovers a tube of lemon-flavored personal lubricant. They then experiment with anal sex, with awkward results, and decide not to try it again.
Related: Emi's path.
This meme crosses over with Portal 2, what with Cave Johnson's quotable rant about lemons.
Psychic Spies. Explanation One of Kenji's many conspiracy theories.
It's Fukin' Lilly!Explanation A song by Youtube user foreverpandering where he's requested to make a short song about Hanako and to not use the word "crispy". He keeps his promise by singing how much she tastes like bacon and then says that Lilly is better than her.
BEST GIRL IN THE GAME
The loss of sex drive often caused by this Visual Novel has been diagnosed as "Katawa Dick Syndrome," or KDS for short.
The word "Din" by virtue of being an uncommon word.
"Six inches lower and you'll see she's actually masturbating" Explanation When the Mishimmie began to receive a lot of pictures of the ladies that were cut off around their waists, this comment began to appear.
That's not what comforting means! Explanation (spoilers) The single option in Shizune's route is whether or not to "comfort" Misha when she comes to Hisao's room feeling depressed. Many people do not equate "comforting" with "let's have sex".
Misha's disability. Explanation Misha's reason for being at Yamaku was ambiguous before the full release and lent itself to much Wild Mass Guessing
The Katawa Shoujo and Madoka Magica girls cosplaying as eachother; Shizune & Sayaka always swap, as do Hanako & Homura ( not withstanding the fact that Homura would actually fit right in with her heart problem), Mami & Lilly usually swap (though sometimes with Misha, coz of the drills), with Rin as Madoka or Kyoko, Misha as the other, and Emi with Madoka or KYUUBEY!!!