The 5th Gen Bumblebee was awesome.
I'm not a fan of Mustangs, but Eleanor from Gone in 60 Seconds is one of my all-time favorite cars.
The General Lee Charger is another all-time favorite
I like the Charger from The Fast and The Furious.
I love the '69 Camaro convertible used in Las Vegas...TV show, not a movie, but still....
Cool cars that weren't really stars of the movie:
The Lexus used in Minority Report was pretty awesome (too bad they never made it for real...concept only)
That TVR that Travolta drives in Swordfish was sweet, as was the Aston used in Die Another Day.
I liked the 91 Camaro Convertible used in Hard Target (sorry, back in the high school/early college days, I was a big Van Damme movie fan)
The Vector that they wrecked in Rising Sun was awesome, although short lived in the movie.