The objective of this article is to systematically present the emerging understanding that 3D porous scaffolds serve not only as structural templates for tissue fabrication but also provide complex signaling cues to cells and facilitate oxygen and therapeutic agent delivery. Strategies in the field of tissue engineering and regenerative medicine often rely on 3D scaffolds to mimic the natural extracellular matrix as structural templates that support cell adhesion, migration, differentiation and proliferation, and provide guidance for neo-tissue formation. In addition to providing a temporary support for tissue fabrication, 3D scaffolds have also been used to study cell signaling that best mimics physiological conditions, thereby expanding our understanding beyond 2D cell cultures. It is now understood that cell responses to 3D scaffolds are distinctively different from 2D surfaces. Recently, 3D scaffolds emerged as a vehicle for improved oxygen transport to seeded cells and also to deliver relevant therapeutic agents to facilitate tissue formation and/or to regenerate damaged or otherwise compromised tissue functions. In this review, our goal is to provide recent advances made in 3D scaffolds to modulate tissue formation, cell signaling, mass transport and therapeutic agent delivery.