Casino Royale (2006) - Daniel Craig at his peak, excellent script and characters, Judi Dench continues to nail it, and Vesper was amazingly tragic.
Goldfinger - This one was just so much fun, most of the cliches of Bond come from this movie, and Goldfinger himself is an absurdly funny villain.
The Living Daylights - Closest to the books, most believable Bond put to the screen here, even now. There' still some of the fun to be had from the Moore era, but no longer with such excess.
HM: Goldeneye (The only good Brosnan flick), On Her Majesty's Secret Service, Never Say Never Again (it was directed by The Empire Strikes Back guy, and it shows)
I like your top 3 choices - Casino Royale was a smash - and as a minimalist story it was still full of action and suspense after the bloat of DAD.
What in particular about the direction of Never Say Never Again did you really pick up on?
I like the chase scene in Monaco - the contemporary house where Bond finds the French agent in the waterbed - and pretty much any scene with Barbara Carrera - she has a sizzle in her scenes that Basinger lacks.
The Domination video game scene is quaint and nostalgic.
Bernie Casey is a fine Felix Leiter - best even.
The MI6 scenes are perhaps the worst part of the movie - terrible casting.
The title sequence is a bit underplayed, the theme is serviceable, and despite a bigger budget than Octopussy - it does not have as much spectacle to it - maybe because it is Kevin McClory's Thunderball with a few small modifications to update it to the 80's.