British Airways. It has to be really really cheap for me to even glance at a non-direct flight or a partner airline.
But I've had good and bad experiences with British Airways, Continental, Delta, AirFrance, Virgin, American, and Air Canada for long-haul flights. It completely depends on the day and what the airline and airport are dealing with. I try to fly mid-week and only direct where possible. I'm lucky, I'm London -> Atlanta is easily direct. I may never leave London and I'd bribe my parents not to leave Atlanta unless they move to another hub city on the East Coast.
American Airlines is my personal worst (BA partner nonetheless!), and I don't see the hype about Virgin.
Last Spring I flew London -> Orlando -> Atlanta when I booked a flight 4 days before travelling. The airline was fine, Virgin, but the Disney goes next to me just about drove me mad with their singing, which seemed to be happening throughout the plane, so I'm thinking that's a no for the future.