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.
In some episodes, after making a large batch of a dessert (such as chocolate mousse) Alton would half-joke that he would probably just sit down and eat the whole thing. Then come episodes like "Herbal Preservation" in Season 7 and "Live and Let Diet" in Season 13..
In the 2001 episode "Scrap Iron Chef", Alton competes with a sweet old lady in an Iron Chef spoof. Four years later Alton became the host of Iron Chef America.
Similarly, one episode of Good Eats is an Affectionate Parody of MythBusters dedicated to "smashing" culinary myths. Jump ahead to 2012, and Alton guest-stars on an actual MythBusters episode.
Alton in a few episodes and appearances on other shows declared that he thought the "umami" craze was largely a marketing stunt and he thought it was pretentious and a little ridiculous. Cue his hosting of The Next Iron Chef, and he was having to hawk Kikkoman soy sauce and its "rich umami flavor".
Harsher in Hindsight: In the Amber Waves episode, he praises the manager of the homebrew shop he visits. A year or two later, Marietta Homebrew Supply closed down because the manager in question was embezzling thousands from the family that owned the shop.
Growing the Beard: The show started hitting a groove after the problematic first season, but didn't really run at its full potential until Alton took over production (and built the now-familiar Good Eats Kitchen) in 2001. This was partially due to space constraints; the white kitchen was a small kitchen in a small house, which made shooting trick shots and gags difficult.
Jerk Ass: Occasionally Alton himself, though intentionally invoked for comedic effect.
Shipping: A lot of fans seem to ship Alton/W. The knowledge that the former is married does not dissuade them one bit. This was lampshaded in the behind-the-scenes episode, believe it or not; the mailman bringing AB his fan mail comments on all the letters asking if W is AB's wife.
The corresponding recipe in the Good Eats cookbook dutifully lists "1 1/2 pounds ground shepherd" among the ingredients for shepherd's pie (with a note suggesting ground lamb or mutton as a substitute should shepherd be unavailable).