Cap Holes Modifier

The Cap Holes modifier builds faces in the holes in a mesh object. A hole is defined as a loop of edges, each of which has only one face. For example, one or more missing faces from a sphere would produce one or more holes. The modifier works best for filling planar holes, but can do a reasonable job with non-planar holes as well.

Note: This modifier can cap holes in a sub-object selection passed up the stack. It caps any part of the hole that's adjacent to, or within the selected geometry, whether vertex, edge, or face.

Tips

If the Cap Holes modifier doesn't appear to work, remove it, apply a Mesh Select modifier to select the faces surrounding the hole, then apply Cap Holes to the sub-object selection.
The Cap Holes modifier creates faces with invisible edges unless you turn on All New Edges Visible before you apply it.

Example: Cap a hole in a sphere:

Create a sphere.
Apply an Edit Mesh modifier to the sphere.
Use the modifier stack to access the Face sub-object level.
Select several contiguous faces and delete them.
Go to the Object level of the stack.
Apply a Cap Holes modifier.

The hole you created are filled.

Tip: Turning on Smooth With Old Faces makes the cap less obvious.