Spa is my favourite, no doubt.
I wouldn't say I have a clear number two, but it's probably between Brands Hatch, Mount Panorama, Ascari, Nordschleife and Silverstone. I never thought too much about Silverstone but lately I've been really enjoying it. I think that track probably gets much less appreciation than it deserves. It might have a little to do with being in the GT Academy demo.
Anyway, I feel sorry for poor Suzuka. Absolutely fantastic track but I think playing Prologue so much took that track's heart away for me. Plus since it was one of the first tracks I think it looks rather bland -- specifically graphically, not as a track. If they remade it to the level of Brands Hatch it might have a new lease on life for me.
I rarely want to play Fuji as well again because of Prologue, and it's also not that strong of a track IMO. That's one thing Suzuka still has going for it. As much as I've played it, there's no doubt it's a great circuit.
I will also say that I don't want to drive on the Nordschleife as much in GT6. Like most people, I raced so much on it in GT5. It's in no way dead to me and it's not quite at the level of Suzuka, but I'd usually rather race on other tracks I think. But again, there's no denying it's a great track and it's hard to actually get bored of it with how much variance it has.