"Baka" is the most frequently used pejorative term in Japanese literature and spoken language, so it easily made its way into manga and anime. It's suspected that the word originally came from Chinese or Sanskrit.
Anime fans often use "baka" like their favourite characters do, as a joke to call their friend a fool or jokingly in discussions about their favourite series.
Some waifus are loved for their use of "baka", like Asuka is. Usually, they are known to be tsunderes and scold the main character (or other love interest they have) a lot. Fans like to create video compilations featuring those waifus saying "baka".
- Asuka's "Anta baka?" used towards Shinji in Neon Genesis Evangelion
- Killua's "Baaaaka" in Hunter x Hunter