There are three basic philosophies that Friar Laurence expresses in this scene, and all have to do with his Fransican background.
As a Fransican, he is dedicated to the care of the soul and his task is to advise pentintents of the ways in which their lives may go off course. Thus, when he rightly (according to doctrine) says, "Virtue itself turns vice being misapplied , / And vices sometime's by action dignified," he is expressing care for Romeo's soul, in that he urges the young man to examine his actions and see where truth lies.
Secondly, he acts as a confessor, a confidant that Romeo can tell his sins to and expect to be forgiven and guided. "God pardon sin," he tells Romeo (2.3.41). Then, he urges Romeo to "Be plain, good son, and homely in thy drift; / Riddling confession finds but riddling shrift, " (2.3.51-52).
Lastly, Fransiscan philosophy dictated that wordly ornamentation led to corruption of the soul; so while Friar Laurence here is not speaking directly of Romeo's attire, he is urging him to cast off justifications for his behavior. He can only expect good advice if he comes to the priest morally "naked."
Of course, we see that the Friar himself is not following his own dictates, but that is for another post.
Friar Lawrence dabbles in the arts of herbology, and he relates to the audience how many plants have not only the power to heal, but the power to kill as well, if they are used inappropriately. In this way, the Friar is philosophising about the duality that exists in the world. People in general are made up of both positive and negative traits; it's the choices they make that determines their character. Shakespeare demonstrates this idea once again when Romeo gives gold to the apothocary to buy poison. Romeo claims that gold is worse than poison to men's souls, but that is if it is used for evil. When used for good, gold can be a valuable tool. The potion that the Friar concocts for Juliet has the power to heal the situation the lovers find themselves in, but its use and fate's intervention that kept Romeo in the dark about the potion led to the destruction of the star-crossed lovers. These events are forshadowed in the Friar's soliloquy about the plants he was gathering from his garden in Act II.