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.
Chick Magnet: Okabe, depending if you view Mayuri's, Ruka's and Faris' feelings towards him as romantic. Overtly the case in the game where each of the aforementioned characters has a romantic ending. The drama CD even adds Moeka to the mix.
Complete Monster: Kurisu's father, who is willing to steal his own daughter's work and then kill her to keep her quiet, all out of jealousy since he can't handle the thought of his own daughter being smarter than him.
Sky Clad no Kansokusha, which sung by Itou Kanako, is already awesome as it is for the 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.
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...
Hilarious in Hindsight: A few weeks after the ending of the anime, CERN published an article about neutrinos traveling faster than light.note Unfortunately (fortunately?), turns out the claim is false.
At the start of the VN, Daru snarks that Okabe's alias sounds like an anime character. Soon, it would indeed be...
Ho Yay: Despite him insisting otherwise, it is hinted that Ruka does have romantic feelings for Okabe, even when he was male. Okabe also sees him as a Stupid Sexy Flanders.
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).
Jellyman report, with pictures of jellified humans who were used as experiment for time machine.
In a similar vein, jellified Mayuri from a later episode.
The threatening email sent from SERN to Okabe, complete with a picture of a severed, bloody head. All of this from a research organization too.
The letter written by the suicidal Suzuha was particularly haunting. Her constantly writing "I failed" and the revelation that she became mentally unstable after 25 years of bliss are enough to induce nightmares.
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.
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.