I've been to a few:
Zesto's (on University, near Rene-Levesque i think)....quite the scenery after 3am. Quite the experience!
Arahova (i believe it's near Du Parc, about 5 or 10 minutes from the downtown area....there's a famous bakery located across the street that's also open 24 hrs)....pretty good place to eat after-hours.
Picasso (near the Chabli & in the same building as Les Amazones)....had breakfast there & enjoyed it.
Dunn's (on Metcalf, near Ste-Catherine)....typical greasy smoked meat joint. Not as good as it used to be about 15-20 years ago. I only go there when there's nothing else open on Ste-Catherine.