Mine would have to be "Serenity".
I also like "Twice Stung" for one reason, this quote...
Joanna Remmings: Oh, I've heard about you. You're the guy that does the whatchamacallits, you know: MacGyverisms.
MacGyver: MacGyverisms?
Pain is merely the weakness leaving the body!
Murdock ones were always good but I love Halloween Knights, it had great thrills and a bit of movie feel to it. The ep where Mac has to fight off thugs in the woods with his dad is solid too.
share"Passages" I love how it is Pete that saves him at the end.
Also, I love any episode with Harry in it. I've loved John Anderson since his "western days" when he was in pretty much every TV western ever made... multiple times as multiple characters.
I've always had a soft sot in my heart for the "Amish Episode" too: "I've died and went to Thanksgiving."
The first one.
I sat & cried (I did the same when the series was done).
I wasn't so unusual after all.
The Eraser
Three for the Road
The Human Factor
Early Retirement