How I will make every password in my user table encrypted(md5()) except one particular row using a single query?
UPDATE table SET Password = MD5(Password)
I will say though that MD5 isn't a very good level of encryption and you should consider something stronger such as ENCRYPT with a custom salt. Read about it here
EDIT: Looks like the original question changed. Here's the altered query to accomodate
UPDATE table SET Password = MD5(Password) WHERE ID!=[specified index]
EDIT: Worth noting
MD5 Encryption Hacked