I do keep mine stock for all intents and purposes:
On the car, I installed an antenna power cutoff switch because the antenna goes up anytime the radio is on, even when listening to a CD and don't need the antenna. (This is a stupid design.) Also I installed some galvanized steel mesh "hardware cloth" over the cooling air intake to keep leaves and debris out of my radiator, which works awesome. Those are the only changes so I still consider the car stock. All replacement parts have been factory equivalents (spark plugs, universal joints, etc).
On the truck, I installed an aFe Pro Dry air filter, not for any imagined performance benefit but because it is a lifetime filter. Also I put a mini UNI air filter over the emissions air pump intake, and a dash cam LOL. Again, all replacement parts have been factory equivalent (water pump, AC condenser). I consider the truck to be stock also.