Leaving aside Minas Tirith and Minas Morgul which have towers as part of their overall structure, there are two very important towers, sometimes called the titular towers of the second book of the trilogy, which are clearly symbolically very important, namely Orthanc and Barad-dûr (Saruman's and Sauron's places, respectively).
But why? Towers are designed to guard and to spy, and both towers seem poorly suited to these purposes. Neither tower is part of a fortification, they are isolated, in the centre of their respective power's territory.
Are they to spy? Again, a tower that is designed to spy is typically built at the edge of a territory controlled by a power, or at the very least on high ground. Both towers are surrounded by mountains in the books (Saruman at least has a decent view in the films).
These towers are clearly not designed merely to protect their occupants and form a seat of power, for otherwise a dungeon or castle would serve better. Clearly Tolkien's choice of tower for these villains is very important, but it is not jumping out at me why.