Apple IIe technical notes. This note presented an overview of the Apple IIe and its differences from the Apple ][ and Apple ][+. The Apple IIe Technical Reference Manual now documents this information.
Understanding the Apple II by Jim Sather. A really detailed look into the hardware and operation of the Apple II computer.
External link (its 82 Meg, hosted by Internet Archive)
Beneath Apple DOS is a great reference for how Apple DOS functions, in detail from the sectoring on the disks, to the boot process, to all of DOS'es functions and calls.