For me it is a "how does it sound" sort of adjustment.
Humbuckers and Lace Sensors I like to run close to the strings. There isn't a ton of magnetic pull from the pickup. Single coil pups have a lot of magnetic pull on the strings and will pull the note out of tune and make really strange sounds if they are too close to the strings. Stratitis is a common term for this.
Lately I've been backing most of my pickups down with good results. I get more tone and I can turn the amp up louder and make it work more. There is better articulation of notes when I've come down. I use tube amps so turning them up works for me.
Fender has a standard suggestion for their guitar pup heights. It can be found on their online set up guide at their web site. Personally I don't think there is a correct height across the board and rely on what sounds best.