The motion of bioparticles in a microfluidic environment can be actively controlled using several tuneable mechanisms, including hydrodynamic, electrophoresis, dielectrophoresis, magnetophoresis, acoustophoresis, thermophoresis and optical forces. These mechanisms are applied to obtain desired bioparticle motions which are important in facilitating different biological processes. In this work, we review the fundamentals, features and applications of these tuneable mechanisms for the manipulation of bioparticles such as proteins, nucleic acids, viruses, bacteria, stem cells, cancer and tumor cells, blood cells and multicellular organisms in microfluidic systems. We focus on applications that can realize biomedical devices potentially suitable in diagnostic, therapeutic or analytical applications. Future perspectives of microfluidic systems incorporating active bioparticle manipulation mechanisms are included.