The idea that a secret organisation, according to the protagonist, is conspiring against him is a similarity. At the same time both series are perverted and both have a somewhat weird/special female side-character.
The main characters in both series also seems a bit awkward when trying to interact with 'normal' people, yet somewhat like a leader among their own small clique/group of friends (which seems to be a coding guy and the weird girl in both series).
Besides that, they also have in common that reality seems somewhat off or twisted to the protagonist. There might be more, but this is
The protagonists in both series believe in the existence of a secret organization that is out there to get them. Both shows display a good balance between comedy and darker themes.
Both feature main protagonists who are slightly nutty, believe in some global conspiracy, and don't like to shave.
Both anime has an evil Organization and both Male leads is somewhat obsess to it and having delusion about it.. and the female leads also helps the male leads to overcome what's happening both anime has a funny side and serious sides..
In both shows, the male leads suffer from the delusion that a mysterious secret organisation is conspiring against him.
The female leads seem innocent and pure at the first sight, but upon closer inspection they have their own tragic stories to tell.
They are both great, have dark psychological humor, and leave you with a strange feeling of happy depression. In any case, they are both worth watching if you haven't seen either one.
While "Welcome to the NHK" and "Steins;Gate" aren't all similar in overarching plot nor animation style, there is something about the "normality" of the two shows that can't be overlooked.
Both are them are set in a realistic, believable world, without over-the-top characters. Dialogue is witty and sensible, and both start off relatively harmless, but eventually delve into the psychological drama type of anime.
The early episodes of Steins;Gate feature a lot of jokes about otaku culture that would fit right in in NHK, plus both shows feature semi-insane main characters who believe that there are secret organizations plotting against them.
Seto and Okabe are quite alike they both made up a conspiracy theory, they are both awkward to strangers, have a bit of a wrong view on the society and they both have their group where they can be themselves. These series have something big simular in the end but guess if I tell that it is considered spoiling.
and except all of this, these are just 2 big masterpieces.
Both feature conflicted over-the-top main characters overcoming obstacles.
Both anime have a dark tone with romance added in. Also both have very funny dubs.
Both anime have a good balance of comedy and dark themes.
Both protagonist believe in the existence of an "organization"
Both anime also have a lovely, pretty and helpful female leads that the protagonists relies on, and they both have tsundere tendencies as well.
They also have sidekicks who wear glasses.
...and although farfetched, the protagonists are also trying to be successful in creating something ( in SG, find a way back to the Alpha world line; in NHK, to create a video game)
Both feature a paranoid MC thinking they were involved in some sort of conspiracy (NHK) and hunted by an evil organization (Steins Gate).
Both anime also have female leads that can understand and empathize with the protagonists and at the same time help them to overcome their problem.
Just like Steins;gate, NHK also starts off rather slow and static and only starts to pick up the pace in the latter part where things get more serious.