Kamen Rider Liger is based on Liger Zero. Kamen Rider Liger is the fanfiction author Kamen Rider Bushido's homage to Zoids' mascot mecha Liger Zero, and each form Liger uses corresponds to one of the forms Zoids' Liger Zero is capable of using.
Suzaku is based on Liger Zero's Fuzor Partner, Fire Phoenix.
Mega's Photon Debugger is named after a particular Keyblade.
Yuji's Karyuu techniques and Elle's Tenryuu techniques are from Fairy Tail.
As stated above, Kamen Rider Showa's armor is one to Higurashi: When They Cry. In fact, he is also one to Moka Akashiya herself, whose eyes also change from green to red depending on how dangerous she is.
Also in the same chapter, Elle mentions her father marrying a Shirohebi, a Weresheep, a Fangire, an Alraune, an Orphenoch, a Tengu, and a Gargoyle. Except for the Fangire and Orphenoch, all the forementioned monsters came from the Monster Girl Encyclopedia. In fact, a lot of the new Youkai featured are taken from the encyclopedia.
Chapter 50: The chapter title, "Trouble(d) Man", is a shout-out to a popular single that was used as the main theme of Darkstalkers, according to Talismo4ever in the post-chapter comment.
Chapter 58: When the barrier hiding Yokai Academy starts to break...
Shiori: "You know, if this was Chicken Little, someone would be screaming..."
Bystander: "OH MY GOD! THE SKY IS FALLING!"
Chapter 61: The chapter title, "The Devils Went Down to the Academy", is both referring to Rias and Akeno and the song "The Devil Went Down to Georgia" by the Charlie Daniels Band.
Chapter 62: When Kiko asks her elder sister Siria about her engagement...