I never use the Emacs custom facility. It puts cryptic (alright, not too cryptic) entries into the custom-set-variables and custom-set-faces lists that are far away from all the rest of the customizations for a given package. Even worse, some packages—I’m looking at you bookmark+—take their existence as license to write data into the lists that they want to preserve across Emacs invocations. That’s particularly annoying because I have my init.el under version control and this causes merge conflicts when I update my other machines.
Happily, Ryan McGeary over at M-x all-things-emacs has the solution. He shows you how to move the custom lists out of init.el (or .emacs) and into another file. You can then load it separately if you like or just ignore it and whatever rogue packages put in it. It’s probably best to load it just in case but it is nice to be able to get it out of init.el.