Was playing Scott Pilgrim

[Kosheh]

so are there any video game references that are actually obscure in the series

ones that are semi-obscure depending on who you are:

vol. 2's opening image is styled in Bonk's Adventure font, and Knives and Ramona's first encounter, "How appropriate, you fight like a cow" - a Secret of Monkey Island reference.

vol. 3, Scott blurts out "I gotta believe!!" - a Parappa reference...admit it, not a lot of you here played it >:{

vol. 5 scott confuses the twins' for "randy and andy katamari" - katamari's obvious but randy and andy are the dragon twins from river city ransom

and in the last book ramona's wearing a headband in one scene that's a throwback to athena's from KoF

oh and
not spoiling where but Knives and Scott do an X-Strike (you know, the double-tech from Chrono Trigger)