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.
Nickelback? I don't think I like Yosuke anymore :P
Those were my thoughts exactly, here's the album in question. http://upload.wikimedia.org/wikipedia/en/c/cc/AllTheRightReasons.jpg
I'm positive the one next to it is "Minutes to Midnight" http://upload.wikimedia.org/wikipedia/en/7/7a/Minutes_to_Midnight_cover.jpg