Damn. I like your list, and I don't disagree with your choices. I just have a little commentary on the cars themselves.
That Lincoln in the Matrix is fucking sweet. Gotta say, one of my personal favorites.
Ferraris in general - badass. That Ferrari....oh yeah. Alain De Cadenet picked a '62 GTB very similar to that as his favorite Ferrari of all time. If you don't know who that is, look it up.
I haven't seen Training Day (I know, pitiful, aren't I?), but a '78 Monte is alright in my book.
Gone In 60 Seconds....that movie sucks worse every time I watch it. Man, talk about a shitty Disney remake of one of the greatest movies of all time. I love Shelby Cobras. I love Shelby Mustangs. That poor thing was neither. It may have been a GT500 at some point in it's life (I seriously doubt it), but what was in that movie was not a Shelby made vehicle. It was a Ford mustang that someone dressed up to try and look like a Shelby.
This is a true Shelby GT500. Not a great picture, but you can see one of the key differences between Ford and Shelby. I even drew an arrow to help.
Here we have a GT350. Very similar to a GT500. I pointed out two differences on this one.
Here we have a Ford mustang. This one has been heavily modified to match the one in 60 Seconds. It is not a Shelby. Nor did the builder intend to look like it. This is a very fast car, both in a straight line and around corners. Quite impressive, but not a Shelby.
Deloreans... These were the best cars ever made that didn't. If you catch what I mean. John de Lorean was a true automotive genius. The design and construction of those cars was 20 years ahead of it's time. Then de Lorean got caught up in some shitty deals with some drug smugglers...and it all came crashing down.
Stay tuned for my top five...this will take some thinking.