These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Awesome Moments: On a meta-level: Jonathan Katz was diagnosed with multiple sclerosis a year into the show. According to Katz, "I was producing a show, and it was too physical a job for me to get from one location to another and I had to pretend I could keep up with everybody. My manager and attorney said, 'In Hollywood you can't be old or sick.'" Katz continued the show through 2002, while also doing work on Home Movies.
Crowning Moment of Funny: Ignoring the various comedians that appear on the show, there's the scene when Ben nearly sets the kitchen on fire in "Thanksgiving".
Dom Irrera in general.
Dude, Not Funny!: In one episode, patient Bob Balaban tells Dr. Katz all the problems in his life right now, including divorce, his cousin committing suicide, losing a lot of money, and a brain tumor. I really don't know what Bob was going for with this, but it wasn't executed in a funny manner at all.
Growing the Beard: Arguably, the later half of season 3 is when the show really improved; the energy level was higher, the father/son tension between Dr. Katz and Ben was lessened, the improvised dialog was more tightly edited to produce the most laughs, and Laura periodically lightened up a bit. In her own way, of course.
Harsher in Hindsight: One of guest Jon Stewart's bits was how America needed a new enemy, now that communism isn't relevant. The episode in question was from 1996; only five years later, America would get an enemy in the form of Al Qaeda. And we can't forget about North Korea...
Hilarious in Hindsight: One episode had Dr. Katz and his son humorously discussing horror movies where the killers were little people. In 2009, Warner Brothers released Orphan.