Daniel Craig and George Lazenby are probably the best at not breaking the adaptation between the films and the stories too much. I've still not seen Quantum Of Solace yet, but Casino Royale definitely showed the darker Ian Fleming Bond from the stories. Daniel Craig fit that well I think, though he's probably not my favourite overall, and I've only seen On Her Majesty's Secret Service once. I can practically only remember the tearjerker.
Partially due to the Nintendo 64, I grew up with Brosnan Bond... it's a matter of opinion obviously, but as Bond he's got some of the best things of Sean Connery, and some of the less obvious, almost cartoonish stuff of Roger Moore. I'd go for Pierce Brosnan, with Sean Connery coming in close. I obviously wasn't alive for the releases of the Connery Bond films, but they're probably the Bond films that grow on you the easiest when you go back and watch the old ones.
Timothy Dalton is good, but I haven't seen Living Daylights in a long time, and he was brought down in License To Kill by the studio trying to make Bond films into Die Hard and Lethal Weapon, etc.. That's not a completely bad thing, but it affected it negatively in more than one way I think.
So I'm going for Brosnan, closely followed by Connery :)