Fifty Shades Of Grey Easter Egg
During the course of solving the third case, after Athena inspects the dead body, Phoenix says "Nice work, Athena. Your face only turned five shades of pale. I was expecting fifty." The comment seems to be a reference to the title of the popular romance novel.
Naruto Easter Egg
In Case 2: Monsterous Turnabout, you may spot references to "Nine-Tails" and people will make comments to the order of "It was sealed away" and "It caused devastation." The nine-tailed beast also does bear more than a passing resemblance to Nine-Tails, the character from Naruto.