The orbital phase theory was applied to the stabilities of the branched isomers (1) of E4H10 (E = C, Si, Ge, Sn) relative to the normal ones (2). The orbital phase prediction was confirmed by ab initio molecular orbital (MO) and density functional theory (DFT) calculations as well as by some experimental results. Further applications to the relative stabilities of other alkane and alkene isomers lead to the preference of the branched to the normal isomers, the neopentane-type to isobutane-type branching, the terminal to inner methyl branching, and the methyl to ethyl inner substitution in the longer alkanes, as well as the preference of isobutene to 2-butene moieties. The preferential stabilization of the branched isomers was shown to be general and controlled by the orbital phase.