We study the moduli space of J-holomorphic subvarieties in a 4-dimensional symplectic manifold. For an arbitrary tamed almost complex structure, we show that the moduli space of a sphere class is formed by a family of linear system structures as in algebraic geometry. Among the applications, we show various uniqueness results of J-holomorphic subvarieties, e.g. for the fiber and exceptional classes in irrational ruled surfaces. On the other hand, non-uniqueness and other exotic phenomena of subvarieties in complex rational surfaces are explored. In particular, connected subvarieties in an exceptional class with higher genus components are constructed. The moduli space of tori is also discussed, and leads to an extension of the elliptic curve theory.