A few random thoughts about Horner from a long-time fan. Personally I wish he is not doping, but it seems unlikely.
Horner has always been a low-key racer who loved to ride as much as any recreational rider. He had enough natural talent that he was able to relax and enjoy his time off the bike instead of focusing strictly on training and diet as many young domestic racers must in order to stay competitive. Just look at the stories about him and In n Out hamburgers, or the pictures of him sitting on the curb drinking a coke instead of warming up.
One thing that first caught my attention with Horner was his apparent outsider status. He was never one of the golden boys with Armstrong and Hincapie, and raced like a mercenary with a chip on his shoulder against the Weisel group.
On his first trip to Europe, he still looked like an outsider, never comfortable with the culture or the team. I think a good circumstantial evidence argument could be made that he did not dope at this time, or at least was not on a team-organized program due to his discomfort and his poor racing schedule. However, that does not mean he was not doing his own thing or slowly learning what was needed as a "professional".
While it's been pointed out here before that Horner had class as a rider in the US peloton -- and that's certainly true -- I don't see that as evidence for not doping. Consider the infamous picture of him and his Saturn teammates Tommy Danielson and Nathan O'Neil riding away from the pack at Redlands. That was largely a tactical fail by the peloton, but hardly a squeaky clean pair of teammates. His opposite on the women's domestic circuit at the time turning in similar results was Genevieve Jeanson.
I'm willing to give Horner a free pass on his Armstrong comments after joining the Bruyneel teams. As a teammate, he cannot be expected to do anything but toe the team line. It is not in his best interest to bite the hand that feeds.
Since returning to Europe, Horner has acted more professional and planned regarding his training and diet. That may extend to doping as well, but I think some improvement or lack of age-related drop can be directly related to this attitude change. He is also doing this current European campaign on his own terms rather than blindly following team requests on his own.
Watching this Vuelta, Horner seems to be racing as an older racer in line with his younger days. He is very smart and gained his two stage wins largely on tactics rather than overpowering the other racers. Horner is a pure climber who can also go well on hilly circuit races, and he is racing his traditional strengths here. As an older racer, it is very evident that he has lost his pop (jump or sprint) but is better at managing his power at threshold. None of his "attacks" have been vicious jumps, but simply maintaining or slowly increasing the power at the opportune time. At his age, Horner should have lost much of his top end but little of his threshold power, and that's what I am seeing.