Carbon isotopes or deuterated version of any phytochemical that is amenable to analysis using GC is applicable. You should consider both the extraction efficiency and detection capability of your selected internal prior to metabolomic analysis.
Before a convenient suggestion, we should know your extraction protocol/methodology, applied derivatization or not, and the target subset of the phytochemical (e.g. alkaloids, phenolics/flavonoids, tannins, saponins, terpenoids, sterols, organosulfur compounds, etc......)
I suggest several IS (3-4) holding varying polarities and belonging to different compound classes instead of a single one to represent comprehensive metabolome coverage...