Sheldon's statement that unresolved issues are like an itch in his brain that he cannot scratch would explain a lot about his obsessive compulsive need for closure seen throughout the series, and described in The Closure Alternative (2013).
Sheldon and Leonard own a "Mythbuster" Adam Savage bobble head doll, which can be seen behind Leonard when he is looking through a junk box.
At the end of the episode when Raj is yelling at himself in the mirror you can see a "to victory" Dalek poster from Doctor Who in the reflection on his wall.
It's revealed that Penny is still fiercely protective of Raj, and presumably Sheldon, Leonard and Howard.
Leonard tells Sheldon he will go downtown to find out who was the owner of the DVD store. However, he wouldn't have to go far - only across the street. That dome outside their window is actually where Pasadena City Hall is located.