The 'S' on his chest (What do you think it is?)

[MatterEaterLad]

Krypto can continue to wear his "S" proudly on his cape, despite being a different species as well as not of the "El"  family...

[Great Rao]

Hey, Krypto certainly was of the El family!  Haven't you ever taken a dog to the vet?  They always give the dog the last name of its human family.

The actual answer:

http://superman.nu/Costumes/designed.php

Face it, the S has had probably about 42 different origins and explanations.  I like all of them except for the Byrne one, whatever it was.  I like the Kryptonian glyph from Birthright; I like the El family crest from the movie; I like the Jonathan-saw-it-in-a-dream/it-was-designed-at-the-moment-of-creation explanation that Maggin used - and I like the Superboy-came-up-with-it explanation.  Because they're all true.