First one that comes to mind is Anthony Anderson in Harold and Kumar. Naturally, that leads to Dude, Where’s My Car? (“And den?”). Then there’s American Beauty. Any others? It has to be a scene at the window, though, not the front counter.
Charlie’s Angels has a short one with them ordering a lot of food and Drew Barrymore fixing the intercom.
That is an excellent scene.
Don’t Tell Mom the babysitter is Dead has two or three such scenes. There’s a Buffy episode in the early seasons with one. I want to say Killer Klowns From Outer space has one, but I’m not 100% sure.
If you’re also willing to accept drive-through scenes from TV shows, there’s this one from the short-lived “Dana Carvey Show” (with Steve Carell).
Wayne’s World has a memorable drive-through scene where Wayne purposely cuts out his voice repeatedly to give the order taker a hard time, implying that the intercom is malfunctioning, and then his order is repeated back to him flawlessly.
Wayne’s World 2 had one. It’s been a long time since I’ve seen it, but I think this is the gist of it: the cashier’s voice keeps cutting in and out on the crappy speaker, so Wayne decides to imitate it. He starts leaving out random syllables when he’s making his order. The cashier still manages to get the order down exactly.
Nice simulpost!
American Graffiti has a few. 
Drive Thru (2007) is an* entire movie *based around these scenes, with “Horny The Clown” offing teens in various unsavory ways.
in case you’re interested. here’s a drive thru prank from Youtube, where the car was apparently empty.
American Beauty’s is a beaut, if I may coin a phrase.
My wife and I have never stopped laughing over the innocuous “FREE NAPKINS!” sign in the background even though it has nothing to do with the scene.
Married to the Mob has Dean Stockwell addicted to a fast-food joint called Burger World, which almost proves to be his demise when Chris Isaak, as the drive-through attendant, comes out with guns blazing and shoots it out with Stockwell and his thugs in the parking lot.
Rings!
Home Fries, with Drew Barrymore. She’s a fast-food worker.
Those were at a drive-in and the OP is looking for scenes at a drive-thru window. There aren’t any carhops at a drive-thru. 
Clerks 2 - I don’t remember it well enough to know for certain if there are any drive-through-specific scenes, but it takes place at a fast food restaurant that definitely has a drive-through.
Menace II Society - Caine gets into a car in a drive-through lane and robs the driver (and makes him buy him a double cheeseburger).
Lethal Weapon 2 - more the aftermath of going through the drive-thru than a scene taking place at one (although it does start there),
Fandango… “Give me three chili dogs and a malt.”
The Wild and Wonderful Whites of West Virginia had a funny scene with Sue Bob going through a Taco Bell drivethrough:
Sue Bob: Yeah, gimme a quesadilla, the steak and cheese fajita only, with cheese and steak only…
Taco Bell: We don’t have fajitas
Sue Bob: You don’t have fiestas?
Taco Bell: I’m sorry, could you repeat that?
Sue Bob: Why’s it on your sign if you don’t have it?
I just saw a rerun of How I Met Your Mother where they flashbacked to when Marshal got the Fiero. His older brothers let him have it if picked up a coffee order form them, naked. Then they went ahead of him and bought out all the lids & trays.
There’s this classic Beavis and Butthead episode.