Bart: How could you Krusty? I’d never lend my name to an inferior product.
The Church Marquee is always great. One of my favorites is “Evil Women: from Jezebel to Janet Reno.”
When Homer’s waffle resembles Mother Theresa(?) he says -
‘Hmmmm Sacrelicious!’
This is my twelfth attempt to post this. I hope it 's worth it
I’ve used it so many times in my life that “sacrilicious” is ALWAYS worth posting. 
Not necessarily “smart” but I bet it made some people go “huh?”:
“I’m the luckiest man on the face of the earth, now that Lou Gehrig is dead.”
From the episode with Chester J. Lampwick (who invented Scratchy), where Bart lets him stay in their basement:
This one is too smart for me.
When the Simpons go to the botanical gardens, there is a sign outside saying “Our Stamen are Pistil”
Lisa laughs and says “does anyone else want to know why that is funny?”
Everyone else says no.
I know stamen are those stalk things inside a flower, but I have no idea why this is funny. Can anyone explain it to me?
“Our Stamen are a Pistil” - stamen and pistil are both parts of a flower, but the joke is a pun on the expression “you’re a pistol” - which means basically “you’re a card” or “you’re too much.”
There was the episode where Homer stopped going to church and the marquee said,
“Today’s Sermon: When Homer Met Satan.”
This topic has become more of a “favorite line” than a “smartest line.” I think it’s all brilliant.
Lisa: This award ceremony is the biggest farce I’ve ever seen!
Bart: What about the Emmy’s?
Lisa: I stand corrected.
Otto: Wow! I’ve never been called an adult before. I’ve been tried as one…
The entire Sherry Bobbins episode. Among the best lyric writing the show has ever come up with.
Ralph: My doctor says my nose would bleed so much if I would just keep my finger out of there.
Chief Wiggum: Ralphie, if your nose is bleeding too much, it’s because you’re picking it too much. Or not enough.
I probably mis-quoted some of those…
Can someone please explain why in the Episode where Homer and Wally Cogan organise a trip to the superbowl moe, wally and homer all tell each other who their favourite team is whilst hiding their mouth behind a beer glass. Is this an American joke for not wanting to admit a support of the Atlanta Falcons or Dallas Cowboys (the teams they mention) or something entirely different?
Homer J, When an animated show is produced, the actors first record all the lines on tape and the animators draw the cels so that the mouths match the voices. Animation takes a long time to do so that particular episode was drawn a long time before it aired. So long, in fact, that they couldn’t have known who was going to be in the Superbowl at the time it was drawn. Therefore they just covered the mouths and dubbed in the correct team names. By hiding their mouths, they don’t have to worry about their mouths appearing to say the wrong team’s name.
Yes, the South Park boys have done some amazingly fast turn around times from drawing-to-airtime but that’s pretty rare.
cheers
The joke of course was that they were bringing attention to this fact by being so obvious about the dubbing, never having mentioned the teams involved before or after that one scene in the episode.
I don’t know if this qualifies as smart but it’s clever. In the episode where Homer plays Odysseus, he has to cross the River Styx. The main joke is that Styx is playing in the background (Lady, I think). But there are skeletons lining the banks rocking to the music, holding up lighters, playing air guitar etc.
There’s one skeleton sitting on the shoulders of another and as Homer passes in front of them the (presumably) female skeleton opens her tattered vest to reveal her (non-existent) breasts.