Where are the root CAs stored on OS X?
The root CAs are stored in:

/System/Library/Keychains/SystemCACertificates.keychain
/System/Library/Keychains/SystemRootCertificates.keychain

Yes, these are OS X keychain files which are opaque, though not necessarily proprietary. You could theoretically use OS X's Keychain Services APIs to get at the certificate data inside the keychain file, but that might be overkill.

If you want a tangible copy of any of the root CA certificates, just select it in Keychain Access, and drag them to the Desktop to make a copy of them in .cer format.

(You can also use Quick Look in the Finder to preview the certificate info).