I noticed that a few months ago. If you are subscribed to 1up, please link this post, since it contains some analysis of the themes.
Sikora and I also noticed that the
main menu music of the Russian MMO Allods Online is similar to that of the Ballad of the Goddess in SS (the harp part in both cases).
Update: Here are the relevant parts of the scores (the first four measures of both themes) to highlight the similarities between the FF4 Prologue and the
ALttP Ending Theme:

Follow the dotted blue lines (I used both Finale 2008 (the music composition software) and Adobe Photoshop CS6 beta to create the image) (note that the FF4 Prologue was originally in B
♭ Major, but I transposed it to C Major (the original key of the
ALttP Ending Theme) for the sake of comparison)
♭ = flat