I always crack up at this one Asian kid in "The Madonna" while the kids at the Challengers Club are singing "Hark, the Herald Angels Sing". His facial expressions are just funny.
And there's plenty of great humor throughout the MacGyver episodes from time to time. "Harry's Will" and "Honest Abe" both seem to have a pretty good share of humor throughout the episodes.
And definitely the whole scene with MacGyver and Jack trying to get the Ming Dragon in "Lost Love" (Part 2, I think) and Mac is trapped in the case and is trying to tell Jack the numbers to punch in- really funny there.
And the ladies in "Faith, Hope and Charity" are pretty funny too.
Mac makes a few funny cracks in "Good Knight, MacGyver" (Parts 1 and 2), especially when Merlin is crawling over him and he comments that he could use some deodorant.
There's a few funny lines in "Unfinished Business"- I like when MacGyver tells Jack, "Most people go out and work for a living instead of dragging their friends from one disaster to another." (may not be verbatim, but something like that.)
And Earl Dent's and Montana's banter in "High Control" is pretty funny too.
And Pete's asking MacGyver to go bowling at the end of "Blind Faith" is pretty funny too.
Oh and definitely- "Out in the Cold"- when MacGyver takes in an injured Pete for a while- there's a bit of The Odd Couple style humor going on- pretty funny.