I'd have to consider The Fly to be his most accomplished film visually, although I find his entire output up to and including Crash completely indispensable. And the films he's done since, although not horror, are fantastic as well. I consider him to be the most prolific and thought provoking horror director of the last several decades.
Loved The Fly. Videodrome. Crash. They Came From Within. But I think I'd have to go with his non-horror flick A History of Violence. Fantastic movie, fantastic performances. Seems like a simple story on the surface but it has so many layers and is loaded with subtext. Viggo Mortensen's never been better.
Yeah A History of Violence is one of his best. Crash is awesome too but I would say Rabid is my fav. I saw Rabid at the movie theater at the time and I remember after watching it I couldn't get it outta my mind for ages and had to told everyone I came into contact with to check it out.