Color

Tints are applied to several blocks, items and particles in order to display a much wider array of possibilities than would be possible with a raw unmodified texture without the need for potentially millions of distinct files.

Grass
Grass blocks have several gray parts on the texture. These are coloured later when rendering, depending on what biome the block exists in. Grass and ferns are rendered similarly.

Leaves
Oak, jungle, acacia and dark oak leaves also change color under very similar conditions to grass, although the color used is usually different.

Water
Water (itself or in a cauldron) is also affected by a tint, although varying less from biome to biome than foliage.

Stems
Pumpkin stems and melon stems also use gray textures by default, which are then coloured depending on their age.

Redstone
Redstone wire has various different power levels it can be in. The higher the power, the brighter red it is, with its off state being a dark almost brownish red.

Constant tints
Birch and spruce leaves do not change color depending on biome, instead applying a constant color tint at all times. Why this is done instead of simply having a coloured texture with no tint applied is unknown.

Lily pads also use constant coloring in a similar way.

Spawn eggs
Spawn eggs have two distinct colours to each of them.

Potions
Potions (and likewise, splash potions and lingering potions) also have colors applied to a white texture. This color can be defined to be anything through commands.