Two that I can think of that weren't mentioned yet are from Magical Shopping District Abenobashi and Magical Project S (Pretty Sammy).
Abenobashi is one of Gainax's newest shows. There are SO many references to other anime, sentai shows, RPG's and other things. First of all, almost all of the character designs are from other Gainax shows. The main male character (can't remember names) looks like Taro from FuriKuri, and the main girl character is Hikari from Eva. Later on there are blatent references to DBZ and Fist of the North Star.
Near the end of Magical Project S, Pixy Misa (the evil magical girl) is seen flying through space in a big space ship. They show her behind one of those huge wooden steering wheels, and she's dressed up as Captain Harlock. Keep in mind that Magical Project S IS a parody show about magical girls. But with the Captain Harlock reference it's hard to figure out who the target audience is.



