Suppose you're doing the byte shuffling right? Or you split the hash value in two and you concatenate them in the reverse order, something like that.
Now here's the thing: if you have a determined attacker, they will figure out your code does that. So you gain no extra security from it
For a casual attacker this may be a bigger deterrent. Now, this casual attacker may try to create (or already has) an account, for which the password is known. So he goes and compares it trying to figure out your encryption mechanism
It's slightly more difficult than the guy that just used MD5 to hash the passwords (let's assume that's the minimum security people use - "in theory")
So, it's all fine and dandy until you have another 'increase the security' idea that actually decreases the security. And this is more common than you think.
Example: taking the hash and encrypting it (for some choices of hash and encryption)
(Not to mention when people think that because they use this 'improved security scheme' that they invented they can be lax in security elsewhere in the chain)