Unfortunately, some of the muscles that could seriously benefit from stretching just can't be stretched. The reason being simply the way we are built doesn't allow for us to contort ourselves in such a way that will apply tensile pressure to some key muscles.
A quick breakdown of some of these muscles and why it would be awesome if we could actually stretch them:
Supraspinatus and Subscapularis (2 of the 4 rotator cuff muscles) - These muscles that are part of the rotator cuff group are often the cause of pain in the shoulder, but unfortunately they can't be stretched effectively. The supraspinatus lifts the arm to the side, so moving your arm in the other direction far enough to stretch is impossible, since your torso is kinda in the way. The subscapularis is attached to the underside of the scapula, sandwiched between the shoulder blade and ribs. No matter how you try to twist your shoulder, the trigger points in the portion of the muscle attached to your scapula will not stretch out. Bummer.
Quadriceps - This one is probably surprising, since we often see athletes pulling their foot back against their backsides to stretch the quads. However, though it feels like you are stretching them, it is only one of those muscles - the rectus femoris - that is stretching. The other three (vastus lateralis, vastus medius, and vastus intermedius) are not being pulled enough to stretch them. Mostly these three muscles don't cause issues, but sometimes the vastus lateralis can be a bit of a troublemaker.
Pec Minor - Or, more properly, pectoralis minor. This muscle can be a major player in serious problems such as thoracic outlet syndrome, and is often the main culprit in pain between the shoulder blades. When