For moduli I would second Geometry of Algebraic Curves, Volume II.
For a clear introduction to stacks, I like Martin Olsson's book "Compactifying Moduli Spaces for Abelian Varieties". A good motivation for studying stacks is Mumford's beautiful paper "Picard groups of moduli problems".
Also there is a book being written on stacks by several authors (Behrend, Conrad, Edidin, Fulton, Fantechi, Göttsche, Kresch) that is extremely clear: http://www.math.uzh.ch/index.php?pr_vo_det&key1=1287&key2=580&no_cache=1