Robert Vanderaarde has released an open source tool built to create texture atlases that support pixel padding. Written in C#, the tool is useful for using a texture atlas in terrain generation. The reason the padding is necessary is that when you create mip maps for the textures, without the padding there is often bleeding on the texture atlas.
The open source tool is available on Github at https://github.com/robertvanderaarde/TextureAtlasPadder.
