Brewing

Brewing is how potions and splash potions are made in Minecraft. Jeb had originally announced that brewing will not come out in 1.9, though it did in Beta 1.9 pre3. It is on it's official release in Minecraft 1.0.

General Guide to Brewing
The player needs to craft a Brewing Stand and right-click on it to display the brewing interface. In the single space at the top, a reagent can be placed to distill into the bottom 3 spaces that can hold any combination of potion and/or water bottles. A brewing process starts when the top space and at least one of the bottom 3 spaces are filled, and is indicated by the column of bubbles to the left animating. At the same time, the brewing progress is indicated by how much the arrow bar on the right fills up. When the bar is full, the brewing process is complete. The reagent is consumed, and the contents of the glass bottles(s) will change depending on the reagent brewed into them.

As long as at least one of the three bottom spaces is filled, the brewing will continue, and additional bottles of water or potion can be added. However, if the reagent is removed, or the bottom 3 slots are emptied at any time during the process, the process will stop and nothing will have been brewed.

Alchemical Components
Alchemical components are supplies used to make potions. All except for the Cauldron are necessary for brewing.

Reagents
Reagents are used in conjunction with the above components to produce a whole array of potions and splash potions.

Base Affecting Reagents
Base-affecting reagents are necessary to create primary and tertiary potions and affect the duration and intensity of a tertiary potion's effects. Gunpowder affects the application of the potion when used (thrown vs. being consumed by the player).

Effecting Reagents
Effecting reagents imbue Awkward Potion with a particular effect and do not affect potion duration or intensity. When brewed with a Water Bottle, any of these reagents will produce a Mundane Potion.

Paired Affecting Reagents
Paired effecting reagents are effecting reagents that create negative tertiary potions when paired with a Fermented Spider Eye.

Primary
All primary potions are created by brewing a single reagent with a Water Bottle and can be combined with Gunpowder to create their throwable Splash Potion counterparts.

Secondary
Secondary potions are created by brewing a reagent with a primary potion and can be combined with Gunpowder to create their throwable Splash Potion counterparts.

Tertiary
Tertiary potions are created by brewing a reagent with a secondary potion or another tertiary potion and can be combined with Gunpowder to create their throwable Splash Potion counterparts.

History
Initially, the Cauldron was where potions were brewed. Code in Beta 1.9 pre2 revealed that Potions were brewed by adding water to the Cauldron followed by certain reagents. Correctly combined reagents would confer purely beneficial potion effects, and incorrect combinations added negative effects. The system was complicated, lacked a GUI, and formed many duplicate potions (i.e. two potions that were exactly the same could be made in several different ways), so Notch and Jeb came up with a new brewing method using a Brewing Stand. The Cauldron's role in brewing was relegated to being a slightly more efficient storage vessel for water. Brewing was greatly streamlined and simplified when a brewing GUI was added and most duplicate potions were removed (the total possible potions went 150 combinations to 25 different potions in 31 combinations). However, this new system made some potion effects available in earlier 1.9 pre-releases inaccessible (e.g. Nausea, Blindness and Invisibility).

Throwable Splash Potions were introduced in Beta 1.9 Pre4 and brewed by placing gunpowder and any potion together in a brewing stand. This pre-release also introduced Glistering Melon as an alchemical reagent to replace the instant health effect conferred by the Ghast Tear, which then added the effect of regeneration instead. This version also converted certain reagents into base-secondary reagents (the Spider Eye, Glistering Melon and Blaze Powder made Mundane Potion when brewed into a water bottle in addition to their previous functions), bringing the potion total to 28 different potions in 35 combinations.

Trivia

 * Only 1 ingredient is needed to brew into up to 3 potions. These three potions do not necessarily have to be the same.
 * Upgrading an Instant Health Potion (I) with glowstone dust has no downsides.
 * Upgrading a Fire Resistance Potion with redstone dust has no downsides.
 * Although Jeb said that in the 1.9 pre-release 3 there were 161 possible different potion combinations with 2,653 in the future, in the actual third pre-release only 22 different potions could be made without the use of external programs. Of those, 19 potions had one of 8 different effects.
 * The Mundane Potion made from redstone has a different metadata (64) than the mundane potion made from any other ingredient (8192). Unlike Mundane 64, Mundane 8192 can be made into a Splash Mundane Potion by adding gunpowder that is, like its base potion, without any effect.
 * Splash potions can be fired by Dispensers.