Class org.bukkit.block.ContainerBlock: in favour of InventoryHolder
Member org.bukkit.block.CreatureSpawner.getCreatureType (): In favour of getSpawnedType().
Member org.bukkit.block.CreatureSpawner.getCreatureTypeId (): Use getCreatureTypeName().
Member org.bukkit.block.CreatureSpawner.setCreatureType (CreatureType creatureType): In favour of setSpawnedType(EntityType).
Member org.bukkit.block.CreatureSpawner.setCreatureTypeId (String creatureType): Use setCreatureTypeByName(String).
Member org.bukkit.command.Command.tabComplete (CommandSender sender, String[] args): This method is not supported and returns null
Class org.bukkit.command.TabCommandExecutor: Remains for plugins that would have implemented it even without functionality
Member org.bukkit.DyeColor.getByData (final byte data): The name is misleading. It would imply Material#INK_SACK but uses Material#WOOL
Member org.bukkit.DyeColor.getData (): The name is misleading. It would imply Material#INK_SACK but uses Material#WOOL
Class org.bukkit.entity.CreatureType: Use EntityType instead.
Class org.bukkit.entity.FallingSand: See FallingBlock
Member org.bukkit.entity.LivingEntity.shootArrow (): Use launchProjectile(Arrow.class) instead
Member org.bukkit.entity.LivingEntity.throwEgg (): Use launchProjectile(Egg.class) instead
Member org.bukkit.entity.LivingEntity.throwSnowball (): Use launchProjectile(Snowball.class) instead
Member org.bukkit.entity.Player.updateInventory (): This method should not be relied upon as it is a temporary work-around for a larger, more complicated issue.
Member org.bukkit.event.entity.CreatureSpawnEvent.getCreatureType (): In favour of getEntityType().
Member org.bukkit.event.entity.CreatureSpawnEvent.SpawnReason.BED: No longer used
Member org.bukkit.event.entity.EntityChangeBlockEvent.EntityChangeBlockEvent (final LivingEntity what, final Block block, final Material to): Provided as a backward compatibility before the data byte was provided, and type increased to all entities
Member org.bukkit.event.inventory.FurnaceBurnEvent.getFurnace (): In favour of getBlock().
Member org.bukkit.event.inventory.FurnaceSmeltEvent.getFurnace (): In favour of getBlock().
Class org.bukkit.event.painting.PaintingBreakByEntityEvent: Use org.bukkit.event.hanging.HangingBreakByEntityEvent instead.
Class org.bukkit.event.painting.PaintingBreakEvent: Use org.bukkit.event.hanging.HangingBreakEvent instead.
Class org.bukkit.event.painting.PaintingEvent: Use org.bukkit.event.hanging.HangingEvent instead.
Class org.bukkit.event.painting.PaintingPlaceEvent: Use org.bukkit.event.hanging.HangingPlaceEvent instead.
Member org.bukkit.event.player.AsyncPlayerPreLoginEvent.disallow (final PlayerPreLoginEvent.Result result, final String message): This method uses a deprecated enum from PlayerPreLoginEvent
Member org.bukkit.event.player.AsyncPlayerPreLoginEvent.getResult (): This method uses a deprecated enum from PlayerPreLoginEvent
Member org.bukkit.event.player.AsyncPlayerPreLoginEvent.setResult (final PlayerPreLoginEvent.Result result): This method uses a deprecated enum from PlayerPreLoginEvent
Class org.bukkit.event.player.PlayerChatEvent: This event will fire from the main thread and allows the use of all of the Bukkit API, unlike the AsyncPlayerChatEvent.

Listening to this event forces chat to wait for the main thread which causes delays for chat.
AsyncPlayerChatEvent is the encouraged alternative for thread safe implementations.
Member org.bukkit.event.player.PlayerCommandPreprocessEvent.getFormat (): This method is provided for backward compatibility with no guarantee to the use of the format.
Member org.bukkit.event.player.PlayerCommandPreprocessEvent.getRecipients (): This method is provided for backward compatibility with no guarantee to the effect of viewing or modifying the set.
Member org.bukkit.event.player.PlayerCommandPreprocessEvent.setFormat (final String format): This method is provided for backward compatibility with no guarantee to the effect of modifying the format.
Member org.bukkit.event.player.PlayerEggThrowEvent.getHatchType (): In favour of getHatchingType().
Member org.bukkit.event.player.PlayerEggThrowEvent.setHatchType (CreatureType hatchType): In favour of setHatchingType(EntityType).
Class org.bukkit.event.player.PlayerInventoryEvent: Use InventoryClickEvent or InventoryOpenEvent instead, or one of the other inventory events in org.bukkit.event.inventory.
Member org.bukkit.event.player.PlayerLoginEvent.PlayerLoginEvent (final Player player, final String hostname): Address should be provided in other constructor
Member org.bukkit.event.player.PlayerLoginEvent.PlayerLoginEvent (final Player player, final Result result, final String message): Address and hostname should be provided in other constructor
Member org.bukkit.event.player.PlayerLoginEvent.PlayerLoginEvent (final Player player): Address should be provided in other constructor
Class org.bukkit.event.player.PlayerPreLoginEvent: This event causes synchronization from the login thread; AsyncPlayerPreLoginEvent is preferred to keep the secondary threads asynchronous.
Member org.bukkit.inventory.ItemStack.ItemStack (final int type, final int amount, final short damage, final Byte data): this method uses an ambiguous data byte object
Member org.bukkit.inventory.ItemStack.ItemStack (final Material type, final int amount, final short damage, final Byte data): this method uses an ambiguous data byte object
Class org.bukkit.material.Door: No longer functions. Do not use.
Member org.bukkit.material.Door.getFacing (): Does not work (correctly) anymore
Member org.bukkit.material.Door.getHingeCorner (): Does not work (correctly) anymore
Member org.bukkit.material.Door.isOpen (): Does not work (correctly) anymore
Member org.bukkit.material.Door.setFacingDirection (BlockFace face): Does not work (correctly) anymore
Member org.bukkit.material.Door.setOpen (boolean isOpen): Does not work (correctly) anymore
Member org.bukkit.material.Door.setTopHalf (boolean isTopHalf): Shouldn't be used anymore
Member org.bukkit.plugin.java.JavaPluginLoader.classes: Internal field that wasn't intended to be exposed
Member org.bukkit.plugin.java.JavaPluginLoader.fileFilters: Internal field that wasn't intended to be exposed
Member org.bukkit.plugin.java.JavaPluginLoader.getClassByName (final String name): Internal method that wasn't intended to be exposed
Member org.bukkit.plugin.java.JavaPluginLoader.getDataFolder (File file): Internal method that wasn't intended to be exposed
Member org.bukkit.plugin.java.JavaPluginLoader.loaders: Internal field that wasn't intended to be exposed
Member org.bukkit.plugin.java.JavaPluginLoader.loadPlugin (File file, boolean ignoreSoftDependencies): Relic method from PluginLoader that didn't get purged
Member org.bukkit.plugin.java.JavaPluginLoader.removeClass (String name): Internal method that wasn't intended to be exposed
Member org.bukkit.plugin.java.JavaPluginLoader.setClass (final String name, final Class<?> clazz): Internal method that wasn't intended to be exposed
Member org.bukkit.plugin.java.PluginClassLoader.findClass (String name, boolean checkGlobal): Internal method that wasn't intended to be exposed
Member org.bukkit.plugin.java.PluginClassLoader.getClasses (): Internal method that wasn't intended to be exposed
Member org.bukkit.potion.Potion.Potion (PotionType type, Tier tier): In favour of Potion(PotionType, int)
Member org.bukkit.potion.Potion.Potion (PotionType type, Tier tier, boolean splash, boolean extended): In favour of Potion(PotionType, int, boolean, boolean)
Member org.bukkit.potion.Potion.Potion (PotionType type, int level, boolean splash, boolean extended): In favour of using Potion(PotionType) with extend() and possibly splash().
Member org.bukkit.potion.Potion.Potion (PotionType type, Tier tier, boolean splash): In favour of Potion(PotionType, int, boolean)
Member org.bukkit.potion.Potion.Potion (PotionType type, int level, boolean splash): In favour of using Potion(PotionType) with splash().
Member org.bukkit.potion.Potion.setTier (Tier tier): In favour of setLevel(int)
Member org.bukkit.scheduler.BukkitScheduler.scheduleAsyncDelayedTask (Plugin plugin, Runnable task): This name is misleading, as it does not schedule "a sync" task, but rather, "an async" task
Member org.bukkit.scheduler.BukkitScheduler.scheduleAsyncDelayedTask (Plugin plugin, Runnable task, long delay): This name is misleading, as it does not schedule "a sync" task, but rather, "an async" task
Member org.bukkit.scheduler.BukkitScheduler.scheduleAsyncRepeatingTask (Plugin plugin, Runnable task, long delay, long period): This name is misleading, as it does not schedule "a sync" task, but rather, "an async" task
Member org.bukkit.World.spawnCreature (Location loc, EntityType type): Has issues spawning non LivingEntities. Use spawnEntity instead.