The Warm Up
Static stretching typically involves a 'stretch' to be held for an extended period of time (typically 30 seconds) such as the typical calf stretch or quad stretch. A dynamic warm up involves active movement to gradually prepare the body for movement and work. Research has shown there is a large difference in both performance and injury prevention when it comes to incorporating a proper dynamic warm up. Static stretching has been shown to provide no benefit to performance, but has also been correlated with an increase in the likelihood of injury. A proper dynamic warm up on the other hand has been shown to reduce the likelihood of injury as well as an improvement in exercise performance.
Recently, the phenomenon of Foam Rolling has become more prevalent in the gym setting. The efficacy of foam rolling is not that it causes the breakdown of scar tissue and adhesions, but rather it preps individuals from a psycho-neurophysioloigcal standpoint. Foam rolling allows the individual to temporarily 'accept' a higher level of pain tolerance and hence potentially an increase in range of movement (ROM) before an exercise. The current research is still split on whether foam rolling provides any strictly physiological adaptations such as recovery.
In general, there is no perfect template that individuals can follow that will give the best results. The variation of individuals as well as their specific goals in conjunction with their lifestyle restrictions contribute to how an exercise program should look like. However there are general principles of progression that ought to be followed.
When considering which exercises to do for each muscle group (Taking into consideration range of movement, contraindications such as pain or discomfort in specific movement planes, sport-specific goals, etc), they ought to follow logical steps in difficulty. The first step in an exercise program is to make sure that the muscle group has an acceptable range of movement as well as the ability to comfortably stabilize and hold various positions. Once this has been achieved, exercises ought to progress to a period of building strength, muscular endurance, and/or muscular hypertrophy. Once this stage in your training has been achieved, the final step (depending on individual goals) would be to generate power (Strength is the amount of force generated to move a load over a distance. Power on the other hand is the force necessary to move a load over a given distance over a given time).
The last phase of the workout ought to involve an exercise set allowing the body to bring its heart rate back down to about 50-60% of your vDot max (max heart rate). Research has shown simple breathing techniques can aid in the recovery of the parasympathetic and sympathetic nervous systems.