I think you're right - people definitely started out with Rodney, and then moved on to John. I know I did. However, I think there's now being a bit of a Rodney renaissance, in the wake of eps like McKay and Mrs Miller! As for dark!John, you might want to look at trinityofone's Four Quarters AU series, which is another example of a John who's very hard to like. Also, what about helenish's Your Inevitable Unhappy Ending (although not sure about the date there, that may have been late 2005)? That was massively influential, certainly for me, in terms of the potential for John and Rodney to have a screwed up relationship - I remember at the time thinking, 'Yes, god, that's how it is.' She was the first one, I think, who really nailed the kind of relationship which has become much more mainstream fanon since then. (At the risk of sounding immodest, on the topic of darker/weirder John characterisation, my fic Second Skin fit your categorization for popular fics, and was definitely part of that trend).

I'd like to bounce some more of these ideas off of you later on down the road (November/December) if you're interested. Absolutely! I find this fascinating. I'm on AIM as yangtzu62, I'd be interested to chat anytime.