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.
Sky Clad no Kansokusha, which sung by Itou Kanako, is already awesome as it is for the Xbox/PC version opening, but when it's played when Okabe speaks to his future self in Episode 23, it adds awesomeness to this scene.
A popular AMV for the anime is set to Florence And The Machine's "No Light, No Light." And it is awesome.
Let's just be honest here and put the whole frickin soundtrack on this list.
A Russian fan went and made a full fandub of the opening song. It. Is. Awesome.
Fridge Horror: If left alone, the Time Leap Machine can create monsters like Yandere Nae.
"Funny Aneurysm" Moment: When explaining the events of the prologue to Kurisu, she asks Okabe who stabbed her. She then guesses that it was him. Fast forward to Chapter 11, when he goes back in time to try to save her, only to end up accidentally stabbing her himself, and suddenly her guess is not so funny.
If you rewatch the series and see all those people sending D-mails, it seems much harsher since you know Okabe has to reverse them in order to save Mayuri.
Okabe's rants about the Organization and people being secret agents becomes much harsher once SERN and the Committee of 300 are introduced and Moeka turns out to be a secret Rounder agent.
The final couple of episodes involving the plot point of Dr. Nakabashi defecting to Russia and bringing sensitive intelligence that could ultimately start World War III. Cue 2013 and Edward Snowden defecting to Russia bringing sensitive intelligence about the NSA...
Kurisu's father stealing his daughter's paper and then either gets her killed or stabs Okabe. Unlike Moeka, there isn't a single point of redemption in his favor. The drama CDs portray him in a slightly better light (though mostly by making his background more sympathetic, rather than undoing any actual course of action).
Rewatch Bonus: Gratuitously so. Only natural for a series about time travel of course. Seemingly innocuous details from earlier on becomes important later on, and the last episode hinges heavily on what happened in the first episode.
Sequel Displacement: It can be easy to forget that it takes place in the same universe as Chaos:Head and Robotics:Notes.
Viewer Gender Confusion: Ruka is very feminine, so much so that Mayuri asks him to try on her cosplay costumes. He also wears a Miko's traditional robes normally.