Crowning Moment of Awesome: "The Battle of Lawndale High" in Anarchy in the Lawn-D, where one almighty all-in brawl between jocks, punks, nerds, queen bees and everyone in between resulted in the downfall of Li's regime.
The exposure and capture of Ken Edwards is pretty awesome in its own right. Daria tricks Edwards into revealing his true colors, and several people throughout the school work to impede him. When it seems like Edwards will escape, Barch charges through a window and tackles him in the ground in quite an epic manner.
Daria standing up to her grandmother and choosing to stay at Lawndale High.
Crowning Moment of Heartwarming: The first episode ends with a flashback to Daria's kindergarten years paralleling the one from Boxing Daria. Instead of chewing Daria out for refusing to get along with the other kids, Jake and Helen tell her there's nothing wrong with being different and someday she'll meet more people who are perfectly capable of loving and accepting her just the way she is. D'aww...
Then there's the parts where Tom & Jane comfort Daria when she begins to crack under the pressure of dealing with her Big, Screwed-Up Family.
Daria choosing to stay with that big screwed up family instead of leaving them for a prestigious boarding school (paid for by her wealthy grandmother) could also count as this.
Double Standard: Amy calls out Daria for not saying anything after Daria notices (without talking to anyone) that the relationship between Erin and Brian is going south. This is after Erin comes to Amy and asks for advice on how to properly cheat on someone with your boss, advice which Amy freely gives. Amy is never once called out on this.
To be fair, Amy's advice is basically "break up with him," so at least she did something about the situation. Daria just found it amusing, until she's forced to see the consequences of it first-hand.
Argubly there's a double standard about the affair itself, since all the blame seems to fall on Andrew (and even Brian and Michele) but notErin. The only person who thinks she's responsible is Jodie, who gets called out for it. Heck, Erin gives a Bitter Wedding Speech where she basically blames everyone else there for all of her problems. She seems to imply that Andrew coerced her into the relationship, but the reader never really saw enough of their interaction to get that impression beforehand.
Ensemble Darkhorse: The fic's version of Stacy is particularly popular, with her developing multiple split personalities and involuntarily switching between them.
Steve the security guard, an original character for the series, has garnered a large following due to his slacker behaviour and general disinterest in doing his job.
Erin Chambers, a cousin of Daria's and Quinn's seen only once in canon, gets a whole lot more exposure and development in this series, including a kinky affair with her boss, a memorable outburst at her wedding and a subsequent brush with alcoholism. As a result, this has become possibly the most popular depiction of the character in Daria fanfic history.
Les Yay: It is Daria fanfiction, after all. The first time Jane meets Daria, she (jokingly) asks if she wants to make out and she's completely obsessed with Amy.
In the fic's equivalent of "Is It Fall Yet," Jane is much more open to Alison's advances. Which makes things a hell of a lot worse for her when she finally comes to the realization that idle curiosity is all it was.
Also, a background character named Aleesha says that she's willing to have a one-night stand with Daria, who declines.