Every time Misaki begs Hikaru to get up, and Hikaru gets right back on her feet. You can tell they have a connection that's much more than Misaki 'controlling' Hikaru.
Icchan showing up to guide Misaki numerous times and to comfort her after her first loss, you can tell he truly cares about her.
Ohjiro saying that he's falling in love with Misaki and how they are seen together immediately after.
Icchan picking Shuko up, carrying her to the Ferris wheel and essentially proclaiming his love for her and asking that she and Misaki move in with him.
When Misaki and her mother finally reconcile, at the end of the anime.
Especially when Misaki wheels her mother to her place before the final match.
Plus seeing Misaki and her mom walking down the street in the second to last scene just brings tears of joy to your eyes. Not only have they been reunited, but the work that Icchan and Shuko started which created Angelic Layer itself is finally complete and Shuko can walk once again.
The final scene with Hikaru leaning against Athena to mirror Misaki and Shuko.
Hatoko running to, hugging and scolding Misaki in the end of Episode 25, as well as thanking her for keeping her promise in the final episode, complete with a cute kiss on the cheek.