Genshiken/WMG

Ohno and Ogiue are inspired by Hiromu Arakawa.
Each of them got different qualities that make them like Arakawa.
 * Like of muscular men: Ohno
 * Grew up in a rural area: Ogiue
 * Manga-ka: Ogiue

The First President of the Genshiken is an alien
He was sent by his species to study Earthlings. So he decided to set up a club dedicated to a popular Earthling interest.

Genshiken and Welcome to The NHK take place in the same universe
I mean, they both take place in a completely mundane Earth. It is very possible that they take place in the same universe as each other. Maybe Satou ends up going to the same College that the Genshiken is in and ends up joining it.
 * Not only is this plausible, this requires a crossover manga/novel/game RIGHT NOW!

Ohno is an older Kiri Komori
Seriously, she looks exactly like her, except a few years older. Presumably, Harumi introduced her to yaoi, and notably, Harumi's pairings are often from the different Gundam series, which are Ohno's favorite. Kiri decided to put her days as a Hikikomori behind her, and thus decided to change her name.

Ogiue is an older Yukimura Kanau
She is surrounded by the creative influences (several mangakas) and the darker influences required for fuyoshi-dom (Loli-Nicchi). Suppose she went to high school in the Touhou region and picked up the local dialect. It's a perfect fit!

Katou from the Manga club is female version of Eddie Sukenari from Kimi wa Petto
Tall. Dark stringy hair. Creepy looking. Total otaku. And there is the same gag with obscured eyes that are shown sparkley beautiful.

Madarame will murder Kousaka on the day of his wedding
He will then partake of his blood and become a vampire. He will then try to comfort Saki, but it will not work and she will commit suicide. He will then be granted his own domain, a twisted version of Shiou University with the clubroom as his sanctum.

Spotted Flower takes place several years after Genshiken
The unnamed husband and wife are Madarame and Saki. The unnamed wife mentions that her old boyfriend was an Otaku who is also a friend of the husband's, just like Kousaka. The husband mentions that he threw away some S&M DVDs because he could not get into them, just like Madarame. These two are clearly Madarame and Saki a few years down the line.