In the episode where Homer’s mother comes back and he flashes back - the young Homer clutches a Pillsbury Doughboy when he goes to bed.
I think the puppy dog, candy store and fireworks factory was the episode where the class went on a fieldtrip to the box factory, and those were the places they passed. You can see the anticipation in the children’s, and teacher’s, eyes as they were about to arrive at the place, then a sudden let-down when they passed. Only to go to a box factory.
I think the box factory just had the line:
Milhaus: Do any of these boxes hold candy?
Box Factory Guy: No…they hold nails.
The Fireworks, Candy, and Puppydog Store is definately next to the old folks’ home. The box factory did have this funny dream sequence (which Bart contributes to TV wasting his mind):
“Class, instead of going to the box factory today, we’re going to…the box factory.”
Mrs. Lovejoy: “They were having S-E-X in front of the C-H-I-L-D-R-E-N”
Krusty: “Sex cauldron?? I thought they closed that place down!”
The line following that was pretty funny too:
Wiggum: Better start in Greektown.
Novus
My favorite line, and I don’t recall the episode:
Lisa asks her teacher in school a question that is, naturally, not expected. It throws the teacher off, and very cautiously - as-if-she-is-being-robbed-at-the-bank, the teacher hits an alarm
under her desk top:
Cut to Principle Skinner: (looking at a flashing red light) Indepedent Thought Alarm! Must be Lisa Simpson."
And I can’t beleive it hasn’t been mentioned before:
Homer runs into his Doppleganger outside of Mo’s.
Homer: ( gaping) My identical twin…(eyes gazing off over his twins shoulder) Ohhhhh, look at the dog with a fluffy white tail.
That was the episode where Lisa becomes a vegetarian, and the dialogue goes like this:
Skinner: Two Independent Thought Alarms in one day? The children are overstimulated. Willie, remove the colored chalk from the classrooms.
Willie: I warned ye! Didn’t I warn ye? That colored chalk was forged by Lucifer himself!
I have to post this 'cause i just caught it five minutes ago (on the inevitable 11 o’clock Simpsons rerun).
When Mr. Bergstrom, the best teacher Lisa would ever have, left on the train for the inner city, he went on the “Afternoon Delight” 
I’m positive I mentioned that one (that’s the “Guy Incognito” bit).
I cracked up when I saw the arcade named, appropriately enough, J. R. R. Tokens
Also, when they got that wonder dog and Bart give Santa’s Little Helper away Homer had the great line of
“Rats! I almost had him eating dog food!”
For me, the fact that he was “Discus Stu” really took the cake.
Any of Homer’s pendants. “School”. “Fall TV”. “Showgirls”.
Also, when Homer needs to call a bunch of people (his relatives apart from Grampa?), he instructs Marge to bring him the phone book, three beers and his conversation hat.
Indeed, he was calling all of his relatives to prove the Simpson gene was just a myth.
In one of the Halloween episodes, Marge says she’s decided to serve friut instead of candy.
“Fruit is nature’s candy.” she explains. Suddenly, someone offscreen throws a plate (or something else breakable) at her head, narrowly missing and smashing against the wall.
Cracks me up every time I see it.
How about the episode where Homer is the food critic, and he is at the dinner table.
Homer: " Marge these porkchops have two movements, shake and bake."
Marge: “But you love shake and bake, you even put it in your coffee.”
Homer: “I have a more experienced palate now.”
Marge: “Okay, whats a pallate?”
Homer: “It’s a special time in a boys life when…YOINK.”
(grabs porkchops and runs)
Kent: Mr. Simpson, how do you respond to the charges that petty vandalism such as graffiti is down eighty percent, while heavy sack-beatings are up a shocking nine hundred percent?
Homer: Aw, people can come up with statistics to prove anything, Kent. Forty percent of all people know that.
I love using that line when someone says something like: “This new whatchamacallit will make our meetings 38% more effective.”
Another, which as of yet, doesn’t seem to be in this thread:
During the episode where Lisa seeks to disprove the legacy of Jebediah Springfield: She stands on stage in front of the gathered throng, ready to expose the truth. Mayor Quimby has a sniper in place to take her out should she start talking. Seeing the hope and joy in everyone’s eyes, Lisa spares them the unseemly truth. A few seconds later, the sniper still shoots. He misses, but he still took a shot at her.
In the Who Shot Mr Burns? episode, at the end where Burns shows up at the town meeting and everyone’s trash talking him, Flanders suddenly stands up and says “I’d like to hear from Sideshow Mel!” To my knowledge, Flanders and Mel have never really associated with eachother, and for him to just stand up and say he wants to hear from him is just weird. Is there a meaning behind this or do the writers just want us to think that?
In a recent episode I saw a store in the background called “Something Wicker This Way Comes”.
Also, “and I keep telling you, you fly boys crack me up!!!” always gets me laughing.