Disposable mechanical media like fine pads and floss you just want to toss and replace. Other mechanical and bio such as sponges and all of the varieties of ceramic media you want to rinse in tank water. Rinsing in tank water keeps any loss of bacteria to a minimum. Of course an established tank stocked full of healthy plants is pretty much a biofilter in itself, not to mention the bacteria in the substrate and on the hardscape and plants. Of course the amount of bacteria you have is dependent on the amount of "food" that's available for the bacteria, but that's another, although related topic.
Long story short, rinse any media you plan on returning to the filter in tank water to minimize loss of beneficial bacteria.