I think the top 4 are(Order of Newest to Oldest)

Casino Royale
Goldeneye
License to Kill
Goldfinger

Sure there were some good ones in between all of those such as Thunderball(the movie that is parodied the most), The Spy who Loved me, For Your Eyes Only and others, but I feel that those 4 are the best. For the most part the stories are unique and non-traditional enough to make them stand out.