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.
YMMV: No Matter How I Look at It, It's You Guys' Fault I'm Not Popular
This leads to the discussion about how Tomoko remains a jerkass, but being worse off in high school may make readers overlook her less savory traits. In the main series, she still has the same jerkish tendencies but she's depicted more pitifully. At present, her only friend attends a different school while she's making no new friends on her own, and she's also a massive Butt Monkey, whereas in the prequel, Tomoko is less pitiful since she regularly hangs out with her only friend and Komiyama, and isn't as much of a Butt Monkey. The main manga also mainly shows Tomoko's point of view while the prequel mainly shows what other people think of her.
To what extent is Tomoko's situation really her fault, and to what extent is it under her control? Does she have some Ambiguous Disorder or is it more self-fulfilling?
Tomoko's classmates typically don't bully or mock her, but they don't take much notice of her either. Though whenever they talk to her, they treat her normally. Even considering Tomoko's own issues, are her classmates more nice or indifferent people?
Did Komiyama really want to reconcile with Tomoko for her sake or did she just want to get close to her crush Tomoki? Or both? Was Tomoko ironically on the right track when she accused her of only craving his cock? On one hand, Komiyama only responded to Tomoko's own overtures of friendship when she found out Tomoki attended their school too. On the other hand, she honestly admitted to Tomoko that she didn't like her back then, and said she hoped they could get along now.
Awesome Music: The opening has gotten very positive reactions. This could be because the music is more for a battle manga then a slice of life story.
Ear Worm: The opening and some of the endings, such as the cover of "Natsu Matsuri" featuring Hatsune Miku.
This has also become a Colbert Bump - a significant number of people have bought copies of the tankōbon (despite not knowing the language) simply to support the authors, which in itself has drawn even more attention to the manga.
The authors even said on Twitter that this act was responsible not only for the anime being made, but also the continuation of the manga itself.
Early on, some fans on 4chan showed they cared by tweeting the authors pictures of their penises, which the authors acknowledged in an omake.
Heck, it's actually popular enough that it is given an English dub and BD treatment by Sentai Filmworks
Harsher in Hindsight: Tomoko's petty annoyances on Tomoki, such as hogging the shower while he's getting sick and playing a prank on him purely on a whim, becomes less funny considering that this behavior is what made him start hating her in the first place.
Hilarious in Hindsight: The manga club guy comments that he draws the same type of face for background characters because it is the easiest for him to draw. Later, Nico Tanigawa would publish Number Girl, a 4-Koma about... clones.
Pokémon X and Y reintroduces the Hex Maniac trainer class - which now bears a striking resemblance to Tomoko (and the Fairy Girl trainer class to Yuu). Much Memetic Mutation ensued.
In Episode 8, the boy who brought Tomoko an umbrella sees Tomoko again, and she tells him her name. He mishears it as "Momoko" and Tomoko freaks out, which is incidentally the name of another character that Monica Rial played, from Ghost Stories.
Hollywood Homely: Tomoko, though less so than most examples, especially by anime standards. For an anti-social shut-in, she actually looks the part, with dull, baggy eyes and regularly making some rather unflattering facial expressions.
The Author Avatars of Nico Tanigawa as little mammals in omakes, the avatar of the female artist in particular. When foreign fans sent them pictures of their penises, she claimed never to have seen one before. She was also bothered by the male writer perving over Tomoko's voice actress recording her lines, and by the conditions of workers in the animation studio.
More Popular Spin-off: It's Your Fault My Friend's Not Popular featuring Yuu began running in January 2013. While it's not clear yet whether it'll sell more copies than the original, it is running in Monthly Joker instead of Gangan Online.
Narm Charm: The opening is so incredibly unfitting that it circles back to being awesome and makes you want to cheer for Tomoko.
Nightmare Fuel: Some of Tomoko's expressions are unsettling, to say the least.
For example: In the first episode where she threatens Tomoki that she would kill herself if he didn't talk to her. With the aforementioned expressions and dark atmosphere, it makes it seem like she would seriously kill herself.
Squick: Tomoko sure is bent on getting her little brother to be attracted to her. Though when he gets up close to her during such a moment (just to show her out) she freaks out a bit.
Tear Jerker: It feels like it was made just for this and it is difficult to keep perfectly dry eyes when reading the manga and/or watching the anime.
Values Dissonance: One of the bigger western gripes with the plot is the overall lack of input from Tomoko's parents, or adults in general, to get her help with her glaring antisocial tendencies. In context, this isn't that surprising: Japan's take on social therapy/counselling is nowhere near as common or acknowledged as the West's.
Strangely enough, Tomoko's current (2nd year) homeroom teacher doesn't seem to have that memo and butts in, trying to get her to open up in very blunt ways, with Tomoko's expressions definitely looking of the "Stop Helping Me!" variety.
The Woobie: Tomoko, pretty much. You just have to feel sorry for a girl who just has no idea how to talk to people without making herself look like a total dork.
Jerkass Woobie: She can also be unsympathetic at times, which shows how she's self-defeating. The fact that she apparently can't read other people's basic emotions, to the point where she interprets an innocent crush as perverse lust (see her incident with Komiyama), makes it easy for her to be extremely cruel and rude to other people, but also a very sad individual to behold.
As of chapter 47 Komiyama is The Woobie as well, what with her being twice humiliated in front of her crush by Tomoko.