Not all have been used in the Anime. Prepare for the really long post:
In the anime, the basic Poké Ball is the most commonly used of all varieties, with other varieties appearing either very few times or not at all. A vast majority of Pokémon are shown to be stored in regular Poké Balls, to the point that large collections of Poké Balls can be seen with no variation among them. Even Ash's Pikachu, the most prominent Pokémon in the anime which spends all its time outside with Ash, has a plain Poké Ball that differs from others only by the small yellow lightning bolt symbol on it, as seen in Pokémon - I Choose You!.
Despite this, the various other types of Poké Ball have been seen in the anime, usually to illustrate a special property about that particular ball. The lack of the different types is unsurprising, however, due to the fact that, when the anime was first created, the games themselves did not even keep track of the Poké Ball that a Pokémon was caught in, and thus, it made no difference in sending a Pokémon out.
The first time that a Poké Ball aside from the normal variation was seen was in EP035, where Ash was given 30 Safari Balls in order to compete in the Safari Game. With these 30 Safari Balls, Ash attempted to catch various rare Pokémon; however, he only managed to capture an entire herd of Tauros. They appeared in Safari Balls in Showdown at the Po-Ké Corral; afterward; however, whenever Ash uses one of his Tauros in a battle, it is sent out from a standard Poké Ball.
The GS Ball was the second of the variant Poké Balls to appear in the anime, this time with a special purpose. This mysterious ball was unable to be opened by Professor Ivy, and served as the reason for Ash's journeys to the Orange Archipelago (to pick it up) and Johto (to deliver it to Kurt), so that what was contained within it could be discovered. Celebi was long rumored to be related to the ball, something which the Pokémon Adventures and game canons verify, while a director of the anime confirmed that, had it not been insisted that Celebi appear in a central role in the fourth movie, the GS Ball arc would have concluded with Celebi being released from the ball and traveling with Ash and his friends.
A Poké Ball after catching a Pokémon in the animeAlso related to Kurt, as in the games, the first non-standard Poké Ball variants, the Apricorn balls, made an appearance in the anime, and several were given to the members of the main cast. All three members of the main cast received Fast Balls in Going Apricorn!, with Brock using his to catch a Pineco shortly after receiving it. In the next episode, Brock received a Heavy Ball, while Ash and Misty received Lure Balls. While Brock's Heavy Ball and Ash and Misty's Fast Balls would remain unused (and have not been mentioned since), both Ash and Misty would use their Lure Balls to capture a Totodile and Corsola, respectively. Another Heavy Ball appeared in Gulpin It Down, where it was used to capture a giant Gulpin, though this was not the one belonging to Brock.
The Master Ball itself has only appeared once as an actual Poké Ball, in Whiscash and Ash, where it was used by Sullivan in a last resort attempt to catch a wild Whiscash. Despite the fact that a Master Ball cannot be escaped from, the Whiscash swallowed the Master Ball, thus preventing capture, and disappeared back into the water. While not a Poké Ball itself, Misty owns a beach ball that is designed like the Master Ball, which can be seen in Beauty and the Beach and A Hot Water Battle.Ash calling out a Pokémon
The Generation III specialty balls have only been seen in cameos, with only the Repeat Ball and Luxury Ball appearing, in the opening of Jirachi: Wish Maker. These balls contained Brendan's Shiftry and Aggron, respectively.
The debut of most of the specialty balls, both from Generation III and IV, came in the ending Which One ~ Is It?, which contained the first appearance of the Great Ball and Ultra Ball, as well as the first anime appearance of the Premier, Heal, Net, Dusk, Nest, Quick, Timer, and Dive Balls.Many other Poké Balls have been shown in the anime; however, most of these are cosmetic alterations alone, such as Poké Balls with gold plating, diamond studded Poké Balls, and Poké Balls with special designs on them, usually to denote an organization.
Most notably, a broken Poké Ball, snapped in half at its rusted hinges, is kept by both Ash and Gary, symbolizing their rivalry.In Mystery at the Lighthouse, it was shown that if a Trainer catches a Pokémon while they already have six on hand, it is automatically sent to the regional professor. This was again demonstrated in Sparks Fly for Magnemite. Sewaddle and Burgh in Pinwheel Forest shows a major difference in what happens after a Pokémon is captured. Instead of being automatically sent to the regional Professor, the Poké Ball is sealed and the button becomes red. The Pokémon is kept inactive until it is switched out by another actively in the Trainer's party.