The title of the episode is a reference to the Who song "The Kids are Alright". An alternate take of the song plays when the Simpsons look at the photos for the first time.
When Homer moves forward to strangle Bart, the music from Also sprach Zarathustra by Richard Strauss plays. This music was also famously used at a significant point in the 1968 film 2001: A Space Odyssey.
The day after Bart is put to sleep in the Clown Bed, he is seen drawing a picture of the bed with the words 'NO NO NO', which is a reference to the Slenderman survival-horror game series.
Marge says she used to grow weed in the room were today is Maggie's bedroom.
When Moe asks Marge if she wanted the "Matte" finish, he signed one of the photos with Matt Groening's signature.
If this episode aired in 2015, then the flashback took place in 2009 in real life terms. In the show's universe, however, the flashback took place in 1984, which was six years before the show started since Bart was 4 and Lisa was 2 during that year.
Marge's hair seems to change length during the flashbacks.
During the flashback, dramatic music plays while Homer strangles Bart, implying that he's doing it for the first time. However, in "Lisa's First Word" and "The Girl Who Slept Too Little", we clearly see him strangling Bart as a 2-year-old.
A business like Fotohut would have been long out of business by 2009.
When Homer shot the pizza at the bar, the shotgun's shell destroyed the pizza, but left the wooden counter intact. A normal shotgun blast would have left a hole in the wood.
Grandma Flanders appears in this episode, and she last appeared in Lisa's First Word, meaning that she finally returns in this episode after 22 seasons of not being shown on-screen.
Also, Bart still has the clown bed that Homer built for him from the same episode, which is destroyed when Bart and Lisa fall on it.