One thing which does annoy me is that the DVD/Blu Ray sets of TOS present them in 'original broadcast order'. For a very long time it was kind of accepted that the best way to watch TOS was production order, all of the videotape releases were presented in this order for example and I remember even seeing them being shown in packages on TV in this order, but for some reason it changed to broadcast order when the DVD box-sets came along and has never gone back. I appreciate the nostalgia value etc in watching them in the order in which they originally went out back in the sixties, but personally I do think production order presents the episodes as a more logical narrative and thus I find myself having to constantly switch back and forth between discs to watch it that way. How irritating! 
