Baking

Bake Button

Perform the actual fluid simulation. Blender will continue to work normally, except the progress will be displayed in the statusbar. Pressing Esc or the "X" button next to the statusbar will abort the simulation. Afterwards two .bobj.gz (one for the Final quality, one for the Preview quality), plus one .bvel.gz (for the Final quality) will be in the selected output directory for each frame.

Bake Directory

Directory and file prefix to store baked surface meshes.

This is similar to the animation output settings, only selecting a file is a bit special: when you select any of the previously generated surface meshes (e.g. test1_fluidsurface_final_0132.bobj.gz), the prefix will be automatically set (test1_ in this example). This way the simulation can be done several times with different settings, and allows quick changes between the different sets of surface data.

Notes

Unique domain
Because of the possibility of spanning and linking between scenes, there can only be one domain in an entire blend-file.
Selecting a Baked Domain
After a domain has been baked, it changes to the fluid mesh. To re-select the domain so that you can bake it again after you have made changes, go to any frame and select RMB the fluid mesh. Then you can click the bake button again to recompute the fluid flows inside that domain.
Baking always starts at Frame #1
The fluid simulator disregards the Start setting in the Animation panel, it will always bake from frame 1. If you wish the simulation to start later than frame 1, you must key the fluid objects in your domain to be inactive until the frame you desire to start the simulation.
Baking always ends at the End Frame set in the Animation panel
If the frame rate is set to 25 frames per second, and ending time is 4.0 seconds, then you should (if your start time is 0) set your animation to end at frame 4.0 × 25 = 100.
Freeing the previous baked solutions
Deleting the content of the "Bake" directory is a destructive way to achieve this. Be careful if more than one simulation uses the same bake directory (be sure they use different filenames, or they will overwrite one another)!
Reusing Bakes
Manually entering (or searching for) a previously saved (baked) computational directory and filename mask will switch the fluid flow and mesh deformation to use that which existed during the old bake. Thus, you can reuse baked flows by simply pointing to them in this field.
Baking processing time

Baking takes a lot of compute power (hence time). Depending on the scene, it might be preferable to bake overnight.

If the mesh has modifiers, the rendering settings are used for exporting the mesh to the fluid solver. Depending on the setting, calculation times and memory use might exponentially increase. For example, when using a moving mesh with Subdivision Surface as an obstacle, it might help to decrease simulation time by switching it off, or to a low subdivision level. When the setup/rig is correct, you can always increase settings to yield a more realistic result.