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.