Oh, shit. I definitely need to add:
Apocalypse Now (theatrical cut)
Blue Velvet
Taxi Driver
and, because Taxi Driver got me thinking about Scorsese:
Raging Bull
After Hours
Goodfellas
The Departed
(I also kinda like Bringing Out the Dead, but it's not one of my favorites by a long stretch. And Shutter Island was great, too.)
I still need to see Mean Streets, Casino, Cape Fear, and Gangs of New York.