Actor Allusion: It's Bart that goes out of his way to praise Jay's show as something everyone should watch (though doing so admittedly makes him feel dirty). Nancy Cartwright voiced Jay's sister, Margo (a role originally for Margaret Cho, but the higher-ups thought she wasn't a good fit).
Broken Base: Some say it's one of the best episodes of the show. Others (including Matt Groening himself, which explains why his name isn't in the opening credits) say it's one of the worst because it's a crossover, Matt Groening promised The Simpsons would be an anti-sitcom filled with all the things that normal sitcoms wouldn't have (and, apparently, that includes spin-offs and crossovers), and most Simpsons fans at the time thought The Critic wasn't a good show.
Groening had no issue with crossing over with Futurama, either on television or twice in comic books.
Of course, Matt Groening did create Futurama, so that may be why he approved of the 3 crossovers between the 2 shows.
Crosses the Line Twice: In Barney's film, we see him introducing himself at what seems to be an Alcoholics Anonymous meeting, but we zoom out and see Lisa informing him he's actually at a Girl Scouts meeting. To which Barney says "Is it, or is it that you girls can't admit you have a problem!?"
Deleted Scene: A cut scene on the Simpsons season six DVD shows the elderly members of the Springfield Retirement Home doing a porno film called What The Poolboy Saw.
Another cut scene showed the Devil from The Critic who's also auditioning for the part of Mr. Burns, who thought he's perfect and made him his understudy.
Family-Unfriendly Aesop: Homer is admonished for voting for the (admittedly lowbrow) movie he enjoys and when he ultimately does vote for Barney's film, Marge smiles with a declaration of "You voted for the right movie." That Homer changed his vote from one he enjoys to one his peers approve of is treated as absolutely a good thing. It is definitely possible that Homer legitimately changed his mind upon watching Pukeahontas but it didn't take much from the fact that Marge expected him to vote for the choice of which she approved.
"Funny Aneurysm" Moment: McBain's Take That at Woody Allen, "I'm a neurotic nerd who likes to sleep with little girls.", originally referencing Allen's marrying his adoptive daughter Soon-Yi, became more cringe-worthy in 2014 when her stepsister Dylan Farrow accused Allen of molesting her while growing up. On the other hand, Allen is still married to Soon-Yi and she's now in her 40's.
Tear Jerker and "Funny Aneurysm" Moment / Harsher in Hindsight: Barney's film about his alcoholism ruining his life (except for the part where Barney mistakes a Girl Scout meeting for an Alcoholics Anonymous meeting), which makes the flashback of how Barney first got drunk (Homer gave him beer the night he was studying for his SATs — and what's worse, Barney was a Harvard-bound genius in his teens) harder to laugh at in hindsight.
After winning, Barney promises to go on the straight and narrow, at which it's announced he also won a tanker full of Duff beer.
Barney:JUST HOOK IT TO MY VEINS!(truck driver obliges with an IV)