Storage requirement and computational efficiency have always been challenges for the efficient implementation of discontinuous Galerkin (DG) methods for real life applications. In this paper, a fully implicit Jacobian-Free Newton-Krylov (JFNK) method is developed in the context of DG discretizations for the three-dimensional compressible Euler and Navier-Stokes equations. Compared with the Jacobian-based methods, the Jacobian-Free approach saves the storage for the Jacobian matrix which can be of great importance for DG methods. Three types of preconditioners are investigated in which the block diagonal preconditioner requires the least storage, while the block LU-SGS and ILU0 preconditioners require more storage but are more computationally efficient. An implicit time-stepping strategy is adopted for the stability of the current solver, which is based upon a hexahedral spatial mesh and the nonlinear solver package Kinsol is used to improve the computational efficiency and robustness. Numerical results demonstrate that the preconditioned JFNK-DG solver can substantially reduce the storage requirement compared with the Jacobian based method without significantly compromising accuracy or efficiency. Furthermore, as a good compromise between efficiency and storage requirement, the ILU0 preconditioner shows the best choice of the preconditioners presented.