This paper presents techniques for generating orthogonal bases of signals with jointly optimized spectra, in the sense that they are made as close as possible. To this end, we propose new criteria, the minimization of which leads to signals with close energy inside a set of prescribed subbands. We present a first algorithm that performs this spectrum balancing and that we apply to Walsh-Hadamard codes. As an example, we build balanced Walsh codes in CDMA comunications. Alternatively, we propose another way to perform spectrum balancing in two steps and that makes use of joint diagonalization techniques. As an example application, we show how balancing of Prolate Spheroidal Wave Functions (PSWFs) can be used to build orthogonal families of brief impulses with flat spectra that are of potential interest for Ultra Wide Band (UWB) communications.