My favorite two models are:
The Scott CPU
https://www.youtube.com/watch?v=cNN_tTXABUA (great book, website is now offline unfortunately: https://web.archive.org/web/20240430093449/https://www.butho...)
An extremely simple non-pipelined 8 bit CPU. The emulator lets you step through tick by tick and see how the machine code is driving an operation. I spend one lecture showing each tick of a bitwise AND and following the data around from the instruction into the instruction register, how the instruction selects the general purpose registers, runs it through the ALU and then moves the data back from the accumulator into a register. It's one of my favorite lectures of the year.
The Little Man Computer - https://www.101computing.net/LMC/
A higher level Von Neumann style computer that helps introduce students gently to assembly where they can fully understand the "machine code" since it's just decimal. We then build an emulator, assembler and compiler for an extension to LMC that introduces the notion of a stack to support function calls.
It's a fun one semester class, not as intense as NAND-to-Tetris but still an overview of how computing works.