Joss Whedon's songs (one about the writers' strike and the other about how DVD extras like commentaries and making-of features destroy the narrative of the original work) come off less like Take That, Us and more like plain old Take That.
Get a Hold of Yourself, Man!: After the first song is over and they're only "half-way through the first shot" Nathan panics and declares "We're all gonna die!" Maurissa slaps him and actually tells him to "get a hold of yourself".
"We won't have those awkward pauses..." in the intro, "Commentary". Humourously, it's exactly synchronised with the other piece of Hypocritical Humor: namely, "Wow! Sarcasm! That's original!", and both are followed with awkward pauses - the one in Commentary! is much longer, though.
Also, Joss commenting on the evils of DVD extras and how they ruin the original narrative, in an over-the-top DVD commentary musical, one of several DVD extras. Although it may have been the extreme overabundance of them that he was complaining about, rather than merely their use.
The song "Nobody's Asian in the Movies" is commenting on a problem to which Joss Whedon's own TV series Firefly contributes.
Simon Helberg is arguably an even better example with his song "Nobody Wants to Be Moist." He even has a tinkly piano solo!
Metafiction: It's a musical commentary track on commentaries. It probably spend more time commenting about how it's not a very good commentary than actually commenting on Dr. Horrible. The most commentary-ish song is Felicia's 'The Art', but that's full of her Blatant Lies and Self-Deprecation.
Money, Dear Boy: invoked Zach's excuse for why he got involved in a musical product in the first place.
Felicia: But it’s not about The Guild I’d be killed If I shilled For The Guild On somebody else’s time Then again, I sort of was killed The-Guild-season-one-available-on-DVD-plus-new-episodes-at-the-Watchtheguild.com-we-also-have-t-shirts Joss:Felicia! Felicia: Catch-the-Guild-fever!
Stacy comments in "Ten Dollar Solo" that the remake of Fame will be better and less depressing than the original. Said remake is directed by Kevin Tancharoen, brother of Maurissa.
In "Zack's Flavour" mentions that the musical doesn't need to be 'pretty' or 'witty'. Compare with the line from The Producers 'Shows should be more pretty, shows should be more witty' from the song 'Keep it Gay'.
Probably embodied best in Nathan's song, "Better Than Neil", a three-minute-long Take That against the main actor Neil Patrick Harris. Although he claims that it's a sea-shanty that he learned from his pirate mother.