EDIT (cause you keep on changing the title)
every single pokeball has been used in the anime
All pokeballs have been used or shown in the anime. To many episodes to explain. An exception to this are the pokeballs that kurt in pokemon heartgold/soulsilver make for you. Because he makes special pokeballs found no where else, and how ash only met him a few times, many of his pokeballs aren't in the anime. everything else though has already been used.
Here is the results for the masterball however:
Yes. There were two cases, one not so much though...
Misty threw a Masterball beach ball at Ash in episodes Beauty and the
Beach and A Hot Water Battle. A real Masterball appeared in the
episode Whiscash and Ash, where a fisherman attempts to catch an
oversized Whiscash, but the Whihscash swallowed the Masterball