really depends on the sound I am after, for a very clean sound with lots of attack, I like using
a bridge humbucker with the volume rolled back a bit.
For more "classic" clean sounds, I use the neck pickup, at best a single coil, but I really like
the middle position on a humbucker equipped guitar with the bridge pickup volume rolled back
a bit or on a strat the positon between the middle pickup and the neck pickup.
For blues cleans, almost always the neck pickup, digging a humbucker there more and using
single coils for clean leads to cut through.
My favorite clean sound is a telecaster's middle position through a Vox AC30 or a Fender Twin.
Btw. for EMG equipped guitars, neck humbucker always or with EMG SA single coils middle or
neck position, otherwise it's just too "hi-fi" for me.