Hiro saying "oh, boy" at the beginning of this episode is a reference to a show called "Quantum Leap" (1989-1993). The show stared Scott Bakula who played the lead character in the series, Sam Beckett. In each episode, Sam traveled to a different time in the past trying to find home and righting wrongs as he jumped to each time. He would be thrown into a crazy senario at the beginning and his response was always "oh, boy."
In this episode, Hiro proclaims that Charlie is "The Marle to my Crono!" This is a reference to the cult classic SNES video game Chrono Trigger (1995).
Lauren Gilmore gives Noah a key to room 108 at the Midland Motel. In an email, writer Aury Wallington said that 108 was a reference to Heroes episode 108 in which Sylar originally kills Charlie.
Noah's professed love for poetry is a reference to Sandra saying in Genesis that she wanted to marry a poet.