Pulp Fiction
Turner and Hooch. I remember a flossing scene, maybe there was a brushing.
That’s absolutely the first one that came to me when I saw the OP. There must be others, but I’m stymied!
There was that terrible scene in Bring It On (don’t ask) where Kirsten Dunst and that awful Donny Osmond-look-alike are brushing their teeth. And flirting while they do it? 
If the toothbrushing is implied but not necessarily shown explicitly [sup]*[/sup]
Truly Madly Deeply
Pretty Woman
*I can just imagine that as a TV rating category “T - contains Explicit Toothbrushing”…
Superman Returns
Stranger Than Fiction
The Long Goodnight
There are probably lots. Probably even toothbrushing after it was in someone’s bung.
My follow-up question is “What was the first movie to feature toothbrushing?”
Truman
Frankie and Johnny. It was a pivotal scene, where they were doing something competely normal and unromantic, but was romantic because it signified her accepting him into her normal life as they watched the world outside her windows. Awwww.
I’ve heard tell that there’s a deleted ‘pissing while romantic interest chats about day’ scene,’ but it’s not on the DVD extras.
Good call!
And that’s a wrap.
Being There
High Anxiety
And Tuco cleans his teeth with his finger in The Good, the Bad, and the Ugly.
Jim Carrey brushes his teeth in his own memorable fashion, in “The Mask”
Damn. I had the image clear in my head, even knew who it was brushing his teeth and just could. not. place. it.
And I even have that watch!
Ferris Beuller’s Day Off - his unconventional, hands-free ‘chew the brush’ method always stuck with me.
Final Cut with Robin Williams.
Bring it On
ETA: Fuck sedoa got there firstest.
Pee-Wee’s Big Adventure
The Groove Tube
The In-Laws (Arkin/Falk)
Viola in “Shakespeare in Love” uses a primitive toothbrush.
The Graduate