The recent development of microfluidic devices allows the investigation and manipulation of individual liquid microdroplets, capsules, and cells. The collective behavior of several red blood cells (RBCs) or microcapsules in narrow capillaries determines their flow-induced morphology, arrangement, and effective viscosity. Of fundamental interest here is the relation between the flow behavior and the elasticity and deformability of these objects, their long-range hydrodynamic interactions in microchannels, and thermal membrane undulations. We study these mechanisms in an in silico model, which combines a particle-based mesoscale simulation technique for the fluid hydrodynamics with a triangulated-membrane model. The 2 essential control parameters are the volume fraction of RBCs (the tube hematocrit, H(T)), and the flow velocity. Our simulations show that already at very low H(T), the deformability of RBCs implies a flow-induced cluster formation above a threshold flow velocity. At higher H(T) values, we predict 3 distinct phases: one consisting of disordered biconcave-disk-shaped RBCs, another with parachute-shaped RBCs aligned in a single file, and a third with slipper-shaped RBCs arranged as 2 parallel interdigitated rows. The deformation-mediated clustering and the arrangements of RBCs and microcapsules are relevant for many potential applications in physics, biology, and medicine, such as blood diagnosis and cell sorting in microfluidic devices.