Except for energetic degeneracy, having an orthogonal set of solutions to the Schroedinger equation means that you've got wavefunctions corresponding to pure states. These pure states correspond to definite and different values of quantum numbers (say, orbital occupation) and have possibly distinct physical properties ( dipole moment, polarizability). Any experimental measurement of an eigenvalue property of a mixture of orthogonal states would measure an average of the quantity in the pure states. Also, having a pure state means that there is a non-zero probability to trap and observe the individual quantum states by themselves. For example, the lowest energy electronic configuration of helium is with the 1s orbital doubly occupied. And that's almost all of what's inside a helium gas cylinder. But there are orthogonal higher energy states, say 2s(2), that may have different values of, polarizability, for example. Contrary to what's above, you can observe different instantaneous values of a property of a pure state at different times. The proper value is given as a time average - the electron density is one example, because it's a probability distribution.
In the case of degeneracy, such as with unpaired electron spin not in a magnetic field, the situation is a little more complicated, because the degenerate orthogonal solutions can mix.
-Jim