Air

Air represents unoccupied spaces. Although it is internally treated as every other block, air cannot be kept in the inventory and can only be destroyed or created by the placement or removal of other blocks. Air and non-solid blocks are the only spaces the player and other mobs are allowed to move within without mods or glitches. The sole exception is the Ender Dragon which can move within Obsidian, Bedrock, and End Stone.

Clouds
Clouds are a purely aesthetic feature. Pre-indev releases had 2-dimensional clouds, while post-indev releases let the player toggle between 3-dimensional and 2-dimensional clouds with fancy and fast graphics respectively, or completely disable them from the video options.

Clouds in Minecraft Pocket Edition are similar to Indev and Infdev.

Trivia

 * It is possible to survive without air, because other non-solid blocks (that aren't fluid blocks) won't drown or suffocate the player.
 * A bug in abandoned mineshaft generation causes 2×3×3 boxes of air in the middle of oceans.
 * Air is the only gas in Minecraft.