This paper is concerned with the modeling of joints with clearance within the framework of finite element based dynamic analysis of nonlinear, flexible multi-body systems. For actual joints, clearance, lubrication and friction phenomena can significantly affect the dynamic response of the system. In this work, the effects of clearance and lubrication are studied for revolute and spherical joints. The formulation is developed within the framework of energy preserving and decaying time integration schemes that provide unconditional stability for nonlinear, flexible multibody systems. Numerical examples are presented that demonstrate the efficiency and accuracy of the proposed approach. The importance of modeling structural damping and limited driving power are discussed.