This paper introduces a new disturbance estimation scheme, and a possible application to relative output stabilization of multiple systems. Using the proposed disturbance estimation scheme, total unknown external disturbance applied to a plant is estimated and compensated. Moreover, the model difference between an actual system and a desired system is also estimated and compensated. For the purpose of general use of the disturbance estimation scheme as an unknown input observer (UIO), a parameterized design method is given, even for the unstable and nonminimum phase systems. For the relative output stabilization of multiple systems, second-order consensus algorithm is additionally used. A case study, simulations, and experimental tests sequentially validate the proposed estimation and control methods.