The sketch that Leonard claims was drawn by Jim Lee was in fact drawn by the famous comic book artist at the show's request.
Stuart states "that's the closest anyone's come to picking up a girl in a comic book store". He himself picked up Penny in the store on an Anything Can Happen Thursday in The Hofstadter Isotope (2009), but he may not count that instance since Penny was ultimately more interested in Leonard.
Alice (Courtney Ford) jokes that she is from Superman's home planet of Krypton. In real life, Ford is married to Brandon Routh, who played Superman in Superman Returns (2006). Ford and Routh would later play Nora Darkh and Ray Palmer in DC's Legends of Tomorrow (2016), who are DC Comics characters just like Superman.
Raj's "Brobdingnagian desk" from The Hot Troll Deviation (2010) is still in Sheldon's office, indicating that Sheldon eventually came to terms with it.