The crypt'ed MD5 hashes have a special prefix which indicates that's what they are.

For the other hashes, the fact that there's no nonce or other value stored alongside them was a strong hint (although it doesn't rule out a site-wide nonce). However, I confirmed my suspicion by Googling one of the hashes: it was on a list of unsalted hashes that had been brute forced (unrelated to this, the password was fairly common).