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okay there’s Manifest and Fringe that come to mind off the top of my head
dunno if this was a pilot or a first episode:

https://wings.fandom.com/wiki/Legacy
@instudio do we see the pilot on Fantasy Island? Or just the plane? Feels like a stretch
I assume Wings and Northern Exposure do, on account of those series normally featuring pilots.
people who operate boats, ships, and motorcycles are referred to as pilots. So that gets you Gilligan’s Island and Then Came Bronson.
@splicer I mean, at a stretch you could count "Steamboat Willie". He's definitely a pilot, but I don't think it's fair to call that the pilot episode of a TV show.
Still from the movie Steamboat Willie. Mickey Mouse is at the wheel of a steamboat, with hills passing in the background.
so yeah I don’t know how specific you want to get here about what “counts”. Is it a pilot if it’s the first episode that aired but wasn’t something made on spec hoping to sell it to the studio?

The things *I* notice and smile at are shows that don’t normally feature pilots where the first episode features a pilot prominently enough that the episode could plausibly be titled “Pilot” or “The Pilot”. It’s all for fun, right?
#Firefly (2004). The original 2-hour pilot episode is titled #Serenity, but the network decided to air the second episode (titled "The Train Job") first.

However, it doesn't really matter which episode you consider the pilot, because every Firefly episode features a literal pilot named Hoban Washburne, played by #AlanTudyk.
Not quite matching your request, but the second episode of The Goes Wrong Show is titled "The Pilot (Not the Pilot)", in which they are presenting a production of a second world war play entitled "The Pilot", and they want the audience to be clear that it is not the pilot!
the plot of Fringe's pilot revolves around a plane. There are scenes with the pilots in that.
Do SciFi pilots count?

And does Star Trek even have a pilot per se, or just helm? @georgetakei, help?

Or Buck Rogers?

I believe both Battlestar Galactica series should fit.
Wings? https://www.metacritic.com/tv/wings/season-1/episode-1-legacy-891623
the pilot of Manifest must* have.

*I can't back this up
in the pilot for "Psych" one of the characters is a pilot, though it doesn't really bear on the plot, and it's only mentioned in passing.
One I don't think many will think of:

Salvage 1 (https://www.youtube.com/watch?v=XUDJ4pJb248)

also:

Blue Thunder
Six Million Dollar Man

Can you guess how old I am? 😄
Agents of Shield, certainly