The Master Genealogist allows any number of names to be recorded. This makes dealing with the many variant names in my one-name study much easier.
The program still suggests that children inherit the "primary" surname from the father, but you can select which one that ought to be, or just edit the surname if you prefer. All the names for an individual appear in the relevant index. Nicknames etc are catered for too.
I'm surprised that other software seems to be lacking in this regard, since most brides in the english-speaking world change their surnames on marriage. Changing the groom's surname would seem to be the same process.