What have been the most well-known songs in otaku culture over

That's actually a good question. I suppose Marisa Stole the Precious Thing was one of the biggest ones for the peak of Touhou relevancy.

More recently Platinum Disco and Renai Circulation seem to be popular among people judging by all the mashups/remixes but I don't know if I'd call them otaku anthems

>>16279999
Twilight by ELO.

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https://www.youtube.com/watch?v=mKp6UrYEzMA
Miko Miko Nurse.
This used to be a big one in Japan, but I don't think many Westerners know about it.

>>16279999
Just to throw it in after OP, AIR had both 夏影 -summer lights- and 鳥の歌 (natsukage and tori no uta), both of which are incredibly well-known for reasons that I don't think I really understand.

>>16280139

This was huge in the US when youtube first debuted. It even had its own wikipedia page. Many of the OG videos have long since fallen off.

>>16280344
http://www.albinoblacksheep.com/flash/mikomiko

Whatever songs that keep appearing on various Nico Nico Douga medleys. Songs like Melt, you, Do-Dai, God Knows, etc.

>>16279999

Still a classic.

Akira and the team were shitfaced when they recorded this.

https://www.youtube.com/watch?v=X_eOpM7qQHo

An otaku classic:

I been wantin to tell you dis for a while
I like your fake blue eyes and your hoeish style
Let's go for a walk
in the park
You can suck my dick in the dark
and just do what I ask,
"Bitch, bend over. Let me ride your backside like dogs do each other. I know that you're with it so don't start frontin. I don't wanna be your man, I wanna MOVE SOMETHIN,"

>>16282435
This.

https://www.youtube.com/watch?v=JB5IIsX0wS4

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>>16279999

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>>16280412
This. The classic ones (that have lots of overlap) are filled with Touhou, Kyoani and eroge songs.

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>>16285139
Forgot to mention IM@S and Vocaloid.

I can only hypothesize, but Nico Nico seemed like a really close-knit community before everyone and their mother in Japan got an access to internet (thanks to smartphones).

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>>16284694

https://www.youtube.com/watch?v=xBaB6UUcRqM