If all you can see is the MD5 hash value, how can you tell that it was unsalted?
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).
CRYPT_MD5 - MD5 hashing with a twelve character salt starting with $1$
So the hashes you see beginning with $1$ are probably salted.
http://codahale.com/how-to-safely-store-a-password/
[Edit: I meant your typical web application mucking about with salts, not their use within properly thought out things like bcrypt]
Salts will prevent the typical rainbow table attack where you have precomputed hashes for a large number of attempts. Salts won't prevent brute force, but bcrypt will make it so that brute force takes too long for a single given user.
The $1 is for MD5, the salt includes that $1 and the last $, so to crypt the text in php you do crypt($password, '$1$salt$'). Use single quotes to prevent $ from turning into variables. $password in this case (according to mtgox) was md5('password string').