Many people are unaware of the fact that the order in which you perform your stretching exercises is important. Quite often, when we perform a particular stretch, it actually stretches more than one group of muscles: the muscles that the stretch is primarily intended for, and other supporting muscles that are also stretched but which do not receive the "brunt" of the stretch. These supporting muscles usually function as synergists for the muscles being stretched (see section Cooperating Muscle Groups). This is the basis behind a principle that SynerStretch calls the interdependency of muscle groups.
Before performing a stretch intended for a particular muscle, but which actually stretches several muscles, you should first stretch each of that muscle's synergists. The benefit of this is that you are able to better stretch the primary muscles by not allowing the supporting muscles the opportunity to be a limiting factor in how "good" a stretch you can attain for a particular exercise.
Ideally, it is best to perform a stretch that isolates a particular muscle group, but this is not always possible. According to SynerStretch: "by organizing the exercises within a stretching routine according to the principle of interdependency of muscle groups, you minimize the effort required to perform the routine, and maximize the effectiveness of the individual exercises." This is what Health For Life (in all of their publications) calls synergism: "combining elements to create a whole that is greater than the mere sum of its parts."
For example, a stretch intended primarily for the hamstrings may also make some demands upon the calves and buttocks (and even the lower back) but mostly, it stretches the hamstrings. In this case, it would be beneficial to stretch the lower back, buttocks, and calves first (in that order, using stretches intended primarily for those muscles) before they need to be used in a stretch that is intended primarily for the hamstrings.
As a general rule, you should usually do the following when putting together a stretching routine: