These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Les Yay: There's a bit of Les Yay between Ohno and Saki, as well as between Sue and Ogiue in the later half of the manga.
Magnificent Bastard: The original Club President, who collected vast amounts of 'information' on the other students as part of a nebulous 'research project'. He puts it to good use in saving the Genshiken and 'persuading' Saki to join.
Because of the 6-year gap in between airings, the third season features an entirely new voice cast, with both Madarame and Kuchiki sounding deeper than last season.
There are some that view Nidaime as this, since most of the new cast are fujoshi and as a result, a lot of chapters have that as a focus.
The Woobie: Almost every member of the Genshiken can be counted as a woobie; however, the standouts are Ogiue and Madarame.
The Scrappy: Kasukabe, for much of the first season, she's pretty much a hateful bitch to everyone but her boyfriend, who she likes primarily because of his looks. She mellows out a bit as time goes on, but she never really gets called out for any of her past behavior, so it comes across as her getting off light.