Although I did not watch the latest BBT episode, I have seen a screencap, and have got the gist of the story line. And a few thoughts struck me. Primarily the fact that I obviously need to get out more, but -
Someone dropped the ball with the costumes, if they were going for something symbolic. Sheldon as the Flash - every time I see him in that costume, I just hear 'Holding Out for a Hero' in my head. But tall, dark hair and blue eyes - I'm surprised he's not the normal wearer of the blue tights. Zach as Superman works nicely - but the payoff of that should have been Leonard as Batman. Granted, he'd look more like Batmite, but still... Howard as Batman throws half of the subtext away. Sheldon as Batman would have been excellent. JP would so rock a cape. Plus, he does the voice.
(Who am I kidding? If the Snark Knight was the one back in black, I might have watched the episode.)
Raj wanting to be Green Lantern to Sheldon's Flash would have been good, given their closer working relationship now. Though, as he and Howard are the ones with the functioning friendship, they would seem to fit better as the pair. (Though if he'd still wanted to be Catwoman to Howard's Batman, that would have been... er, disturbing.) Relegated to Aquaman - well, he really is the Zoidberg, now. It would not surprise me if he gets dropped to guest star, or worse, in a Season 5. The 'Friends' reboot is gearing up with the three-on-three coupledom, and he's not even the Gunther.
(Slightly more deranged and random thought - when I talked about the SpongeBob/BBT xover, I thought Raj would make a good sea-horse. Nickelodeon for the win.)
Leonard as Green Lantern... eh, well, one could hope that it shows he's prioritising his friendship with Sheldon over thinking with little leonard, but I doubt it. More likely a shout-out to the next DC franchise to hit the big screen.
If Penny had wanted to be a blonde JLA superheroine, she could have been Black Canary. (Leonard could have been her Green Arrow then - that ended well *snerk*.) But making her the female member of the primary JLA Trio, and then fumbling the third member, dilutes the joke. Plus, I can't help but remember that magazine cover the cast did. We all remember who played Superman to her Wonder-Woman in that. (And then there was the lone Marvel interloper.) Similarly to the occasion where JP and KC were disco-ball and dimbo, while the short guy was the mutt. It pisses me off that someone somewhere quite obviously knows where the emotive draw is, and will use it cynically and blatantly to manipulate an audience, since there is never any intention of following through, and then the fanbase is called crazy and delusional to their faces. Unfortunately, I assume that the next unpleasant thing to happen will be some kind of LePer reunion in time for February sweeps.
So, maybe I overthink things. But I just don't think you can take iconic figures and not expect people to apply subtext.
(edit: ...Big, blue and dumb makes me think that Zach should be the Tick.)