I can think of two: As Good as it Gets and It Could Happen to You.
There’s got to be thousands, right? So why can’t I think of any?
Office Space.
My Big Fat Greek Wedding, sort of.
He notices her and is obviously interested in her as she’s a waitress, but they don’t get together until she’s gone on to other things.
Enough with J. Lo. Not exactly in the ranks of the aforementioned flicks, but she played a diner waitress.
The one that pops to mind for me is The Hitcher with Jennifer Jason Leigh as the waitress Nash and C. Thomas Howell as Jim Halsey. It doesn’t go too well for the waitress, as I recall.
Untamed Heart Marisa Tomei and Christian Slater
Arthur Liza Minelli and Dudley Moore
It Could Happen To You Bridget Fonda and Nicholas Cage
Wow. I came in here specifically to mention this (I literally thought of it immediately) since I didn’t expect anyone else to have seen it and/or be brave enough to admit to it. My hat is off to you.
Terminator, sort of.
White Palace with James Spader and Susan Sarandon
Frankie and Johnny
Though Pacino was the cook, does that count or do you want customers?
The Postman Always Rings Twice
In Bad Santa, Lauren Graham’s character is a bartender.
Mystery Men, but then who wouldn’t fall for Claire Forlani?
Petrified Forest with Bette Davis as sweet innocent waitress, Leslie Howard as the faller in love and Humphrey Bogart as the mobster (I mean he is Humphrey Bogart after all).
The Man Who Shot Liberty Valance both John Wayne and Jimmy Stewart fall for the lady serving food.
Harvey Girls with Judy Garland. Basically, that was the whole basis of the film.
Adaptation with a yummy scene with Judy Greer.
Monster’s Ball with a yummy scene with Halle Berry.
The Cooler with multiple yummy scenes with Maria Bello.
The Game though Deborah Kara Unger doesn’t get any yummy scenes.
Sideways with Virginia Madsen, who doesn’t need a scene to be yummy.
Naturally, none of the waitresses I ever meet resemble Greer, Berry, Bello, Unger, or Madsen. 
And definitely not Five Easy Pieces
Anchors Aweigh has a slight reversal on the idea. The waitress Pamala Brittian falls for the geeky guy (Frank Sinatra) and ends up winning him.
Boy Meets Girl with Jimmy Cagney, Pat O’Brian and Ronald Reagan had a weird sort of play on this too.
Fast Times at Ridgemont High, if a pizza place at the mall counts. (The character did wait tables.)
Mystic Pizza
Car Wash
Wages of Fear: Pretty much all of the guys in town are in love with the barmaid.
Oh! Thelma and Louise and Alice Doesn’t Live Here Anymore, which spawned the sitcom.