The "third eye" part is a spiritual reference. Depending on who you ask it has different meaning. To me it is mostly a representation of enlightment and how we dont only see with our physical eyes. We as human beings see through our soul and with emotion. Our eyes dont see the whole picture so our "third eye" (mostly depicted as an extra eye in the center of the forehead) acts as the true sight of what goes on around us.

Anyway, Common broke it down with the line.

- My third eye is like pink eye. Seeming contagious.

He was actually sayin that the way he sees things (through his third eye) is catching on. He has either brought some kind of change in the way his fans see the world or he has meet people who have similar views and he spreads them through his music. Thus the "seeming contagious" part at the end of the line.