I've wondered the same thing. I have a '79 CB650 that I drive every single day. I've gotten to the point where I stopped looking for 650 parts and am trying to fit parts off other bikes to my 650. The alternator will hopefully be my first success. I'm trying to install a CB550 alternator on my 650, since the 650's rotor seems to be so unreliable.
About the popularity thing, the 1979 650 looks a lot like the previous models, while teh 650C and later models look like more of the '80s styling of cruisers. Higher tank, lowered seat, etc. I personally like the looks of the later 650s better, but like the performance of the '79 a lot better.