The best way I think to say it is that shelfs are content specific, whereas Step I and II cover everything.
There are a number of basic science shelfs, which are used differently by each school. My school doesn't use them at all, an ex-girlfriend's school uses them only if you failed the school's exam, one friend's school uses them as their main form of exams.
Then there are the clinical shelfs in the most common 3rd year clerkships - Internal Medicine, Psych, OB/GYN, Surgery, Pediatrics, Family Medicine and I think Neurology. These are much more widely used, but not all schools require their 3rd years to do all of those clerkships - usually the difference lies in whether family med or neurology is involved. My school requires family med, but not neurology, my friend's school requires neuro, but not family med...