Yuu's friendship with Tomoko gives much needed spots of light in her universe.
In chapter 3 of the manga/episode 2 of the anime when Tomoko noticed that Yuu was upset she took her to the arcade where they used to hang out in their middle-school years to cheer her up. And while Tomoko at first lied to Yuu about enjoying her time in high school, when she realized that something was still bothering Yuu she blurted out the truth and tried to raise Yuu's spirits. What happened immediately afterwards kind of ruined the moment; however, the scene still shows that Tomoko doesn't just think of Yuu as a Lust Object but actually cares about her as a person.
In chapter 64 Tomoko again shows that she actually cares about Yuu. In that chapter Yuu is upset that she can't have fun with Tomoko and Kotomi on a beach because it is closed, and eventually starts to cry. Tomoko then apologizes to Yuu for picking this particular beach, and she and Kotomi promise to take Yuu to a better beach next time. They keep their promise in the very next chapter. Chapter 65 also has a Friendship Moment between Kotomi and Yuu, as Kotomi tells Yuu that without her she and Tomoko would probably just waste their summer break away and have no fun; in response Yuu assures Kotomi that she had a lot of fun hanging out with Kotomi and Tomoko.
Although Tomoko feels embarassingly pitied by it, the way her little cousin Kii-chan cares about her is rather sweet.
The cicada shells.
Really, any scene between young Tomoko and Tomoki... which retroactively becomes a Tear Jerker considering their relationship now.
In an odd and strange way, her rivalry with Komiyama. They are so shy, that having someone to fight against feels like an improvement.
The female Student Council President noticing her all alone during the school's cultural festival and getting into a mascot costume to hug her.
In chapter 42 the same Student Council President notices that Tomoko's teacher unwittingly embarrasses Tomoko in public by questioning her on whether she had made any friends. She then comes to Tomoko's aid by declaring herself to be her friend.
Her dad, finding her sleeping in a compromising scene, gently puts her in bed, without waking her up, and tidies up her room.
In the spin-off, Yuu had suddenly achieved popularity when going to school without her glasses and braids. The next day, she puts them back because she found it difficult talking to her true friends with so much attention drawn to her.
The rare occasions when Tomoko manages to talk to someone without embarrassing herself (such as in chapters 37 or 44), and the fact that during the second year of high school she actually makes an acquaintance in her class, are themselves heartwarming, but especially heartwarming are the implications of all of this: that Tomoko does actually make some progress at socializing, even if only at a glacial pace.
Episode 6 of the anime has Tomoko trying and failing as only she can to get someone to go watch fireworks with her. Finally, at the end of the episode, she just goes to a desolate roof she used to hang out on...only to discover some middle school boys were planning on hanging out there. Tomoko is about to leave, but then timidly asks if she can stay and hang out with them. The boys say they don't really mind so she stays to see the fireworks... and to peep into the rooms of the next door love hotel, which is what the boys came there to do. Something about the boys calling her "Onee-sama" is heartwarming, as she bonds with them over being Peeping Toms
When Tomoko has her umbrella ruined and is stuck under a roofed waiting area with two guys her age, she proceeds to embarrass herself in front of them when she tries (and fails) to not make a fool out of herself. Notably, the guys don't mock her, and the friendlier of the two even comes back to hand her a new umbrella (which he bought with his own money). He leaves it by her side when he finds that she's fallen asleep. Too bad Tomoko never really realizes that someone did an unmotivated act of kindness for her.
If it is any consolation, she does meet up with one of the guys in a later episode, who mentions the above. Too bad she tried reading too much into it, and how she used him to try to impress her cousin.
In episode 12, Tomoko tries a new tactic of trying to get the students to talk about her by doing stuff the same way the Student Council President does. However, her first attempt fails miserably, when she squishes a roach in the class, and the students are disgusted by it rather than proud of her. She then tries to approach the president and talk to her casually, but a gust of wind provides Tomoko with a Panty Shot of the president, embarrassing her to the point of running away before she could utter a word. Two students then approach from the other side of the walkway, and ask the president who that girl running away was. She tells them a little about Tomoko, saying she's a cute girl who she'll need to keep an eye on.
At the end of the episode, we get another scene like the first scene, where Tomoko is looking at the definition of an Unpopular Girl again...except this time she ends up laughing at the term and says it doesn't matter, one can interpret this as her finally finding confidence in herself.
Chapter 57: Tomoko and Komiyama haven't noticed, but Yuu and the readers saw something...
The end of Episode 5, when her mother calls her phone and tells Tomoko to come home so they can eat sukiyaki. It reminds her of the warmth a family home can give, especially comforting when she feels obviously lost and out of place in the red light district.
Chapter 62: Tomoko's joy after learning how to ride a bike.
Chapter 68 had Tomoko have a pretty good day at school. In fact, all her inner monologue about how feudal era girls could have spent their time (watching other lords get it on with each other) led her to a passing grade on a pop quiz.