A: Fire stones are under lava in the Overworld, water stones at the bottom of oceans/bodies of water, leaf stones in tree leaves (you'll know when you see it), thunder stones in mountain biomes (can usually be seen on the outside walls).
Master balls? TMs?
A: Master balls along with TMs are dropped by boss Pokémon.
Can I heal Pokémon without a diamonds/healing table?
A: Yes, if you sleep in a normal bed for a night.
How to craft pokeballs?
A: Hammer discs on anvil by left-clicking with a hammer until you get lids. Lid + button + lid= Poké ball!
Check the wiki for an in-depth guide.
A: No. An abnormally small or large Pokemon will remain abnormal permanently. A Pokemon's size stat will even carry over after evolution.
Colored Pokémon names!?
A: These are boss Pokémon; they drop special loot. The order is Yellow, Red, Blue, Green (Yellow dropping the most and green dropping the least).
Please add my favorite Pokémon!
A: Currently the team of Pixelmon is working on Generations 2-5. Please be patient. Note the Generation 6 will not be worked on until Generation 7 is released due to potential copyright issues.
Where do I find Mew?
A: Very rarely in a Jungle biome.
Pokémon in the End/Nether?
A: No Pixelmon-related items/creatures will be implemented in the other dimensions.
Have IVs/EVs and shiny Pokémon been implemented?
If my Pokémon is a shiny and evolves will it remain as a shiny?
Attack not working properly!
Attack missing its effect!
None of the attacks have animations!
A: Not all attacks have been properly programmed in yet. We are working as fast as we can, and the problem will be resolved eventually.
How do I breed Pokémon?
A: This feature hasn't been added yet, but is planned and will be soon.
Programming and Modding Help:
A: Pixelmon is incompatible with Not Enough Items which means it's incompatible with Feed The Beast.
Making a custom map, can I make Pokémon spawn in certain biomes/areas?
A: To make Pokémon spawn in specific biomes, you can edit the database, but the staff are not allowed to tell you how to do so. To make Pokémon spawn in specific places, a Pixelmon Spawner can be used.
Please add more so we can help newcomers out.