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When doing ordinary renders with Cycles, you can get diffuse direct and diffuse indirect passes with one render by filling out the checkboxes.
When you bake with Cycles, as far as I can tell you have to bake one type of pass at a time for each pass you want, and Cycles has to do the same sampling of the scene over and over again to get each pass.

Am I missing some way to bake more than one pass at a time using the same set of samples, or is it simply a limitation of Blender?

Ideally I'd like to check the passes that I want to bake and save them in an OpenEXR multilayer file, then add them up in the compositor afterwards to get the maps I need.

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We are facing a similar problem and I am currently investigating the same issue. In our automated lightmap process we use the following workaround to get the indirect and direct light information without having to bake two passes (we still bake 2 passes but one takes a split second).

Maybe this could be a solution for you:

  • Bake a combined map with x samples
  • Bake a color map with 1 sample (that is enough to get the full information)

  • subtract the color map from the combined map (via node setup or photoshop)

  • problems: if your textures/materials are too dark, you loose information due to the subtraction and overexposed black pixels

I am planning to make a feature request to combine the passes, since it takes significally longer to bake two passes rather then baking a combined pass. Maybe you would like to be a part of it?

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