Guides

Basic

• Download and Installation
• Pixelmon Tutorial
• Poké Balls
• Catching Pokémon
• Training Pokémon
• Evolution
• Items
• Recipes
• Controls
• Commands

Advanced

• Achievements
• EV Training
• Natures
• Fossils
• Shiny Pokémon
• Boss Pokémon
• Legendary Pokémon

Other

• Wiki markup language cheat sheet
• Assorted guides can also be found on the Pixelmon forum here. If you think a certain guide is missing, you can make one there as well.