Treat any class that has a racial substitution as favored for that race. Treat classes that are based along the same concept as the races listed favored class as favored...
For example:
Changelings - Favored Class Rogue - Racial Substitutions Rogue, Wizard, & Psion
treat all of the following as Favored: Rogue, Spellthief, Lurk, Wizard, Psion, & all other rogue-like classes.
If feel this is still too restrictive, you can expand it to treat classes similar to racial substitution classes as favored as well, thus including Sorcerer, Erudite, Wilder, & maybe Archivist.
Alternatively you can simply ignore the multiclass penalties all together and either ignore favored classes as a result, or offer a bonus of some kind for racial classes...