Arcane University:MindTex 2 for Skyrim
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MindTex 2 is one of the many automated texturing tools, others are included in modern 3d software as modules. It can also be used to overhaul existing or algorithm-created textures. Usually, it gives out DDS or png files, however its best to do some post-processing in Gimp or Photoshop to adjust the 5 channel PBR layers to the 2 or 3 channels being used in Skyrim's texture sets.
You can find details of the export formate and necessary settings on the page Arcane_University:DDS_Data_Format.
