All three have the same meaning. The difference is in their usage.
'Yes' is standard English and to be used when you are responding formally, in a mail or speaking to someone.
'Yeah' and 'Yep' are both informal and can be casually used when you are speaking or writing to friends, family etc.
Just to let you know, most dictionaries say that 'Yep' was first used in the years between 1830-40 and 'Yeah' was first used in the years 1900-05.
Cheers.