The names of Jr.'s assistants Mary and Shelley are an obvious reference to Mary Shelley, the author of Frankenstein.
At one point, Albedo refers to MOMO as "my little pêche". "Pêche" is French for "peach", and "momo" is Japanese for "peach" as well.
One of the minor characters in the U.S version of the game is called Professor Hakase. "Hakase" is a Japanese term meaning "holder of a doctoral degree".
Shion Uzuki shares her surname with Citan Uzuki a character from Xenogears (1998), the spiritual predecessor to the Xenosaga series.
This game was a planned 6 part story, but it was ultimately cut down to 3 parts. This is probably due to the financial cost of 6 games, and the "decent," but not "extraordinary" sales.