Clearly this will depend on the type of compounds you are analyzing (volatile/semivolatile, polar/nonpolar/active/reactive etc...)
In EPA labs the standard MS performance check compounds are bromofluorobenzene (BFB) for volatiles (typically purge-and-trap instruments) and decafluorotriphenylphosphine (DFTPP) for semivolatiles. The general technique is to prepare a solution such that 50ng or less of the appropriate compound are introduced to the GC. The key m/z's in the mass spectra are compared to a set of criteria to confirm that the instrument's sensitivity and resolution are acceptable. The mass spec is then retuned if necessary. BFB and DFTPP give information on mass spec performance only. Semivolatiles performance checks include the active compounds benzidine and pentachlorophenol. The relative response and tailing behavior of these compounds is a good indicator of the overall condition of the injector and the column. A dirty, degraded, or highly reactive system will show severe tailing and significant to total loss of response for these compounds.