My favourite Bond movies (no particular order):
OHMSS
Casino Royale
Probably a couple like FRWL or Goldfinger
Tomorrow Never Dies (honourable mention)
I thought QoS wasn't very good at all, lots of action, very little substance. I liked the ending with the Canadian agent, and I liked Bond mentoring the woman wanting revenge.
Skyfall was significantly better than QoS IMO. The ending was a little bit weak but still good enough to not topple the whole film.
I really liked the woman's acting, the one who betrays her boss, the scene where Bond spots that her bodyguards are keeping an eye on her behaviour rather than purely guarding her safety. I liked the general, 'unusual for Bond movies' plot (ie. the whole of MI6's security is compromised). I liked M having a semi-skeleton in her closet, depending on one's point of view.
However the computer element was almost as weak as in the film Swordfish - I mean, FFS, they've just retreated to (essentially) a minimal, tech-free-as-possible bunker because they know their systems have just been massively compromised, but a) they give network access to a computer belonging to a hostile agent and b) the cell holding said agent is controlled on the same network (when the agent is known to have very decent computer skills), and c) why is the cell purely controlled by computer? I can understand some level of computer control/monitoring of the cell, but does the computer doing that even have to be on the same physical network as the rest? Then the whole "ooh, let's give a 3D display to a virus-type-thing" and Bond spotting some sort of password, and I give this segment a solid 5 stars for sheer WTF'ness.
Some people will probably question my need for realism on this point, but IMO it would be like Bond suddenly being able to do bullet curving a la the film 'Wanted', or the stupid bloody invincible car scene in 'Die Another Day'. I'm fine with a bit of computer fictional trickery, like some sort of device that can auto-hack almost any computer on a network like in Iron Man 2 (as long as it isn't used to bridge otherwise huge plot flaws), but the sort of sheer bullshit like in 'Die Hard 4.0' with spotting a heat signature from a building over the Internet or the encryption system that wasn't encryption at all in 'Die Hard 4.0' again, or 'backing up all the important stuff on the Internet' in 'Die Hard 4.0' again, sorry, way too far.
I have Casino Royale, Tomorrow Never Dies and OHMSS on DVD. I'm not sure about Skyfall, I might pick it up cheaply at some point.
I loved OHMSS and Casino Royale because they portrayed Bond to be much more human while not turning him into a love-sick puppy or something distinctly non-masculine.
I liked bits of Goldeneye, though Famke Janssen's character who goes all orgasmic at the oddest moments was just a bit weird and 'this is what the writer thinks someone into BDSM might be like'. I loved Bond's first encounter with M in that movie, I suspect it set the scene for Casino Royale's relationship between M and Bond.