I usually make variables and let others decide for me whether to "upgrade" them. Another criteria is try to imagine it's there's any scenario where a program might way to set that variable automatically. If there is, I'll make a normal variable (and then again let other custom.el lovers worry about the upgrading). Else I'll do the defcustom myself. If I'm creating a very similar variable in form and function to another one, I'll follow whichever style it has.

João