Here are a few for starters: 

The cript of Christine's father is a symbol--the family name is DAAE pronounced "die" and she undoubtedly thinks of death as a friend having been orphaned and tormented with internal and external conflicts through the opera, her musical training, and her purpose in life.

The Opera itself is a symbol.  It symbolizes sanctuary for all the orphans and escapees--the phantom, Christine, other dancers and actors without any other place to go.

The mask the phantom wears is a symbol.  It is is safe-haven outside of the catacombs of the opera.  His way of hiding the hideously deformed face from society--his beautiful face to go with the beauty of his musical talent.

Music is a symbol--it is the hope and life-giving blood of so many, but especially the phantom and Christine.  The phantom's voice has come to Christine in many hours of need.  She has clung to it as her father told her on his deathbed that he would send her the Angel of Music to look after her in his absence.  Music is the connection between the phantom and Christine, and the phantom has trained her secretly for years developing her lovely voice.