One reasonable way to number orbitals is according to their irreducible
representation in the point-group of the molecule---that is, all
orbitals with the same irreducible representation have consecutive
indices. We will refer to this scheme as Pitzer
Ordering.
If the orbitals are the result of an SCF
or some similar procedure, then we will typically order them
within each irrep according to their energies.
A related issue is how to number the irreps. While any consistent choice will do, the most reasonable standard would be to use Cotton ordering, which means that the irreps are ordered according to their order of appearance in the character tables of Cotton's well-known book, Chemical Applications of Group Theory.