(Barely-public documents like patent filings don't count.)
The original 6502 had many undocumented instructions. Most of them not very interesting, but certainly undocumented. http://nesdev.com/undocumented_opcodes.txt
Here is a detailed examination of undocumented Z80 behavior. http://www.z80.info/zip/z80-documented.pdf
The 8080 had undocumented instructions too.
So now we are all the way back to pdp series. The pdp-8 had plenty of undocumented instructions.
Should we go back further? It doesn't stop.
Same was true with pretty much all non microcomputers through the 80s.
Here's a typical datasheet from Rockwell, for example:
http://archive.6502.org/datasheets/rockwell_r65c00_microproc...
It's also worth noting that the architecture diagram on page 5 of this document isn't entirely accurate, either. It's closer to a programmer's model than an RTL description of the CPU; some "hidden" registers used during certain operations (like indirect addressing modes) aren't shown.
Bitsavers has the documentation for the PDP-11/40 I used to have here. http://www.bitsavers.org/pdf/dec/pdp11/1140/. It includes microcode listings both assembled and as flow charts. My PDP-11 had actually been modified before I got it with the microcode ROMs in ZIF sockets, as someone had been writing their own microcode.