With shaders you can:

• Make surfaces/volumes behave in certain ways ingame (water, lava, nonsolid, etc..)
• Blend multiple textures together in various ways
• Create surface sprites (useful for grass etc.)
• Create blended terrain
• Create scrolling, rotating textures.
• Make textures glow ingame
• Provide lighting to your map (light-emitting shaders)
• Combinations of the above