This is the second part of a series of papers devoted to develop Homotopical Algebraic Geometry. We start by defining and studying generalizations of standard notions of linear and commutative algebra in an abstract monoidal model category, such as derivations, etale and smooth maps, flat and projective modules, etc. We then use the theory of stacks over model categories introduced in \cite{hagI} in order to define a general notion of geometric stack over a base symmetric monoidal model category C, and prove that this notion satisfies the expected properties. The rest of the paper consists in specializing C to several different contexts. First of all, when C=k-Mod is the category of modules over a ring k, with the trivial model structure, we show that our notion gives back the algebraic n-stacks of C. Simpson. Then we set C=sk-Mod, the model category of simplicial k-modules, and obtain this way a notion of geometric derived stacks which are the main geometric objects of Derived Algebraic Geometry. We give several examples of derived version of classical moduli stacks, as for example the derived stack of local systems on a space, of algebra structures over an operad, of flat bundles on a projective complex manifold, etc. Finally, we present the cases where C=(k) is the model category of unbounded complexes of modules over a char 0 ring k, and C=Sp^{\Sigma} the model category of symmetric spectra. In these two contexts, called respectively Complicial and Brave New Algebraic Geometry, we give some examples of geometric stacks such as the stack of associative dg-algebras, the stack of dg-categories, and a geometric stack constructed using topological modular forms.