For Fenders, the pickup height "spec" is about 1-2 64ths more than the string-height "spec".
Bass Side <==> Treble Side
Vintage style 8/64" (3.6 mm) 6/64" (2.4 mm)
Noiseless™ Series 8/64" (3.6 mm) 6/64" (2.4 mm)
Standard "J" or "P" 7/64" (2.8 mm) 5/64" (2 mm)
Special Design Humbuckers 7/64" (2.8 mm) 5/64" (2 mm)
See the section on pickups at:
http://www.fender.com/support/basses.php
Mine are close to "spec", but have a bigger than "spec" gap on the low-E side, which seems to give good string-to-string balance.