Just thought I'd get a thread going, I've noticed a few this already in the story mode.
In Charlie's (damnit! that's his name!) room that he has a Catherine calender.
In Yosuke's room his bike has "ATLUS" on it, also on the left side of the screen above his desk I've noticed 2 of the album covers on the CD rack; Nickelback and Linkin Park next to each other.