OK, my three:
Casino Royale, Living Daylights and For Your Eyes Only.
BTW, it's interesting how many people commenting in this thread are pro-Daylights, even though it's currently coming in 7th-ish. (Siomilarly FYEO, which is a bit further back).
If there were more than three choices, then I'd probably have gone for Goldfinger, OHMSS (I'm in the 'If only Connery had done it' camp, though that's assuming it's good Connery not bored Connery) and Spy Who Loved Loved Me (it's a production line Bond vehicle, but it's a production line vehicle where all the parts fit, the paintwork's perfect, it starts on the first turn of the ignition key, and you don't even need to adjust the seat).
After that, probably From Russia, Goldeneye and World is Not Enough. Plus Moonraker, which is rubbish but so rubbish that it's fun.
The duds? Thunderball - bad editing in the final version. Octopussy and View are both dull. And Quantum of Solace feels as if they shot a better, longer film, and then edited out everything except the action sequences.