When customizing my character's outfit or selecting a vehicle, why do some items have the Third Street Saints logo next to them?
They're DLC items. Maybe you've got them as a preorder bonus:
If Saints Row: The Third was pre-ordered, this DLC was added for free.
Battalion Pants are from Explosive Combat Pack.
Reality Climax Pants are from Funtime! pack.
Space Princess Tights are from Warrior pack.
Witch Pants are from Witches and Wieners pack.
And some of them also include vehicles.