As opposed to a main account, a side account is usually an account used to troll online boards or can be used to hold things that cannot be held on a main account; like an extension of the main account.
Eg. 1: That person is obviously a troll and that person is obviously using their side account, I wonder what their main is...
Eg. 2: I can't have anymore Neopets on my main, so I'll just make a side account to hold some more pets!