There's a scene in Silent Hill 3 in the Dark Office Building where a lone wheelchair is visible from a great distance, illuminated by a single light. Word of God has confirmed this is a shout out to the memorably creepy "Hello...Gordon" scene from "Session 9".
In Origins, you can win the "Codebreaker" outfit (SH3 Vincent's vest) by inputting the Konami Code. Additionally, the Collector outfit makes Travis look like Gordon Freeman and the Explorer outfit is evocative of Indiana Jones.
Shattered Memories has a movie theater which contains arcade machines for Contra, Gradius and Rush'n Attack.