Here’s a run-down of all of the comic book mentions in Season 2 of The Big Bang Theory. (I previously did the same thing for season one.)
Episode 1, Sheldon and Leonard, hallway conversation while returning home:
Sheldon: I.e., I couldn’t become Green Lantern unless I was chosen by the Guardians of Oa, but given enough startup capital and an adequate research facility, I could be Batman.
Leonard: *You* could be Batman?
Sheldon: Sure. (scratchy voice) I’m Batman. (normally) See?
(This line returns later in the episode in a very funny context I won’t spoil.)
Sheldon, at Howard’s home while he’s trying to get to sleep, starts talking about how he ranks the women who’ve played Catwoman (although that’s really a movie list, not pure comics). “That makes Halle Berry my 5th favorite Catwoman. … She did make a fine mutant in the X-Men movies, though.” Which leads to a list of favorite mutants. “No, wait, Nightcrawler.”

Howard and Sheldon
Episode 2, discussing Leonard’s lack of love life:
Leonard: What about that girl last year at Comic-Con?
Koothrappali: Doesn’t count.
Leonard: Why not?
Koothrappali: What happens in costume at Comic-Con stays at Comic-Con.
Sheldon also wears a Green Lantern t-shirt.
Sheldon expresses his dislike of Leslie Winkle to Penny:
“Leonard is upstairs right now with my arch-enemy. … The Doctor Doom to my Mr. Fantastic. The Doctor Octopus to my Spider-Man. The Dr. Sivana to my Captain Marvel. … It’s amazing how many super-villains have advanced degrees. Graduate schools should probably do a better job of screening those people out.”
(This sequence sent me into coughing hysterics.)
Sheldon, consoling Leonard: Look on the bright side.
Leonard: What’s the bright side?
Sheldon: It’s only nine more months until Comic-Con.
(I totally agree with those who think the show really needs to do an episode set there.)

Leonard and Sheldon
Episode 3, Sheldon wears a faded Flash logo t-shirt.
When Sheldon is answering Penny’s gaming questions, his friends are confused:
Koothrappali: It’s like some kind of weird comic book crossover.
Howard: Like if Hulk were dating Peppermint Patty.
Koothrappali: I always thought Peppermint Patty was a lesbian?
Leonard: No, that’s Marcie. Patty’s just athletic.
Episode 4, Sheldon is bitter about Koothrappali getting a write-up in People magazine. His friends are telling him to smile, to show he’s happy for him. Sheldon puts on a scary rictus grin.
Howard: Oh, crap, that’s terrifying.
Leonard: We’re here to see Koothrappali, not kill Batman.
Howard: Try less teeth.
Left home while Koothrappali parties, the guys talk about what they want in a friend to replace him:
Leonard: Let’s see… Money, women, technology … ok, we’re agreed, our new friend is going to be … Iron Man.
(Although not truly comics, I must also mention Sheldon’s Greatest American Hero t-shirt in this scene, which I covet.)
Episode 5, as Sheldon’s bumming rides from his friends, he says they can’t go straight home on Wednesdays because it’s New Comic Book Day. Later, Howard borrows a driving simulator he’s created for the Army to help Sheldon learn to drive. When he tries to configure it to be something other than a Humvee, the options are Bradley tank, transport truck, and Batmobile, but they end on “red 2006 Ford Taurus on the streets of Pasadena.” (Penny gets to play airbag with a pillow, another unexpectedly hilarious moment.)

Sheldon and his new grad student
Taking Sheldon to the comic book store is again used as a way to get him to do something in episode 6; in this case, lecture to prospective students, which he concludes abruptly because the new Batman comic is out. Reference is also made to a “humorous footnote” in one of his papers where likens an effect to the Flash playing tennis with himself. In another scene, his new grad student catches him reading Batman #680 behind a textbook.
This isn’t comics, but I have to mention that episode 7 starts with the geeks playing Klingon Boggle. Sheldon also wears a blue Superman logo t-shirt. Later, Penny is warned not to get into it with Sheldon, because he’s “one lab accident away from being a super-villain”, but when things continue, Leonard tells her what “Sheldon’s kryptonite” is. Use of such leads to her being warned that “with great power comes great responsibility”.
(Irrelevant note: I disagree with Marvel and DC when it comes to spelling “superhero”. I don’t put a hyphen in it — unless it’s the Legion’s name. But super-villain for me is always hyphenated. Maybe because KC once told me the story about how the comic Giant-Size Super-Villain Team-Up was referred to around their office as “Marvel Triple Hyphen”.)
After nothing in episode 8, episode 9 has Sheldon breaking into Leonard’s Facebook account, but justifying it by saying, “It’s hardly hacking when you use the same password for everything, Kal-El.” In episode 10, he wears a Captain Marvel logo t-shirt.
Episode 11 has one of the most substantial dialogue sequences with an opening in which the guys argue about Superman’s laundry.
Sheldon: Your argument is lacking in all scientific merit. It is well-established Superman cleans his uniform by flying into Earth’s yellow sun, which incinerates any contaminant matter and leaves the invulnerable Kryptonian fabric unharmed and daisy-fresh.
Howard: What if he gets something Kryptonian on it?
Sheldon: Like what?
Howard: I don’t know, Kryptonian mustard!
Sheldon: I think we can safely assume that all Kryptonian condiments were destroyed when the planet Krypton exploded.
Koothrappali: Or it turned into mustard Kryptonite, the only way to destroy a rogue Kryptonian hot dog threatening Earth.
Leonard: Raj, please, let’s stay serious here. Superman’s body is Kryptonian, therefore his sweat is Kryptonian.
Howard: Yeah, what about Kryptonian pit stains?
Sheldon: Superman doesn’t sweat on Earth.
Howard: Ok, he’s invited for dinner in the bottle city of Kandor. He miniturizes himself and enters the city where he loses his superpowers. Now, before dinner, his host says, “Who’s up for a little Kryptonian tetherball?” Superman says, “Sure,” works up a sweat, and comes back to Earth, his uniform now stained with indestructible Kryptonian persperation.
Koothrappali: Boo-yah.
Sheldon: Superman would have taken his uniform to a Kandorian dry cleaner before he left the bottle.
Koothrappali: Kandorian dry cleaner? I give up. You can’t have a rational argument with this man.
In episode 12, we see Sheldon’s GL t-shirt (from episode 2) again, and when Howard gets upset, he holes up in his bedroom with a stack of old DC comics (including a 1980s Wonder Woman and a comic from the Death of Superman era). Meanwhile, Leonard talks to Penny about “that overexposed to gamma rays thing” she’s got.
Penny: What does that mean?
Leonard: You know, like most of the time you’re the easy-going Bruce Banner, but then when you get angry, you kinda turn into, you know, like RRRRRRR. (Makes gritted-teeth face.)
Penny: I turn into a bear?
Leonard: Seriously? Gamma rays, Bruce Banner? You didn’t get the Incredible Hulk from that? … Never mind.

How to Make Friends Flowchart
Episode 13 features Sheldon, standing in front of a flow chart with a final box marked “Begin Friendship”.
Leonard: Sheldon, there is no algorithm for making friends.
Howard: Hear him out. If he’s really on to something, we could open a booth at Comic-Con and make a fortune.
(Surprisingly, if you follow the flow, it’s not a bad process.)
He also wears a different Flash t-shirt from the one in episode 3.
Episode 14, Sheldon explains why he has some spare money to loan:
Sheldon: I see no large upcoming expenditures, unless they develop an affordable technology to fuse my skeleton with adamantium like Wolverine.
Penny, incredulously: Are they working on that?
Sheldon: I sincerely hope so.

After Sheldon has previously explained he has different hiding places for his money, and one of them involves a superhero action figure…
Leonard: But if you’re ever short, there are always a couple of 50s in Green Lantern’s ass.
In episode 16, Sheldon reports that the new issue of Flash is out when he returns from the comic book store. Then he talks to it. “Hello, fastest man alive. Wanna see me read your entire comic book? Wanna see it again?” This episode originally aired on March 2, 2009, and the issue he’s holding is the The Flash #247, the last Wally West issue, which came out December 2008 (on Christmas Eve). There wasn’t another one between then and the episode, which suggests a high level of attention paid to these kinds of details.
The Flash costume from season one makes a reappearance in episode 18 after Sheldon has too much coffee late at night.
Yet another Flash shirt, a long-sleeved jersey type, is worn by Sheldon in episode 19. The guys also have another debate:
Koothrappali: I like Green Lantern, I’m just saying it’s pretty lame that he can be defeated by the color yellow.
Sheldon: Only the modern Green Lantern is vulnerable to yellow.
Leonard: Golden Age Green Lantern was vulnerable to wood.
Koothrappali: Great, so I can take them both out with a number two pencil?
(Perhaps my favorite comic book dialogue exchange in the entire series so far.)

Penny visits the comic book store
I’m not even going to attempt to tackle episode 20, which has all kinds of references as the group visits the comic book store. It may just have the most (accurate!) comic references of any sitcom episode ever.
In episode 21,
Sheldon: I’m just in a good mood. While my compatriots are in Las Vegas, I will be enjoying a blissful evening in my personal Fortress of Solitude.
Penny: That’s Superman’s big ice-thingy, right?
Sheldon: You know, I’m in such a good mood I’m actually finding your tenuous grasp of the English language folksy and charming today.
Episode 22 takes them back to the comic store, where Sheldon says, “Smell that? That’s the smell of new comic books. Oh, YES.” He then gets into an argument with Stuart over whether calling the new issue of Hellboy “mind-blowing” is a spoiler or not. And the Green Lantern shirt returns again in episode 23. He also wears other, non-comic t-shirts multiple times in this season, making for a realistic, limited wardrobe typical of someone who doesn’t care much about clothes.
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