Hi, I very rarely post here, but I feel I can contribute.
I've put many pickups in my JS, and I think the most versatile humbucker I've used was a Seymour Duncan "Custom Custom". It seems to only do one thing... sound exactly right for anything (in my opinion, obviously). The JB was good but somehow not as much at home with clean tones, it's very hard to explain, it just felt to me that the CC was better. I hear good thing about the "Custom Five" too. You could also try sticking in a Dimarzio Tonezone for some just plain WEIRD sounds, really mid-heavy, I kinda liked it.
...as for neck pickups I only tried two, one that came out of a "mystery strat" and was just plain horrible, I only installed it to see if it was any good cos the strat was missing most of its parts. The other one was a hand wound one made 30 years (or so) ago by a local amateur guitar builder, and I just fell in love with it it was overwound and REALLY warm and bluesy, so I never changed it. As a result I can't fairly recommend anything properly. I hear really good things about Kinsman stuff though.