From the ground up? Well, there's always the source:

http://www.intel.com/content/www/us/en/processors/architectu...

For learning assembly? For MASM I enjoyed this book years ago:

http://www.amazon.com/Assembly-Language-Intel-Based-Computer...

For GAS something like this might be more appropriate:

http://www.amazon.com/Professional-Assembly-Language-Richard...

Patterson & Hennessy is used a lot in colleges to teach low-level architecture and assembly:

http://www.amazon.com/Computer-Architecture-Fifth-Quantitati...

The shallow end of the pool is simple RISC CPUs e.g. Atmel 8-bit AVR. The complete instruction manual is something like 160 pages (compare to x86 at 3k+) and there are tons of beginner resources for doing assembler on those chips.

There's more structured material for MIPS than AVR. Plus the AVR has some funky memory maps and modes.

This all time classic from MIPS is a good starting point: "MIPS R4000 Microprocessor User's Manual" [1]

[1] http://groups.csail.mit.edu/cag/raw/documents/R4400_Uman_boo...

There is a developer friendly virtual machine called Bochs. It can be hooked to a debugger so you can see what is happening. I prefer DDD for debugging hooked to GDB (backend).

Here is an assembly cheat sheet that I like a lot: http://www.jegerlehner.ch/intel/

Also GCC can output assembly if you want to see what simple C code looks like in assembly http://stackoverflow.com/questions/137038/how-do-you-get-ass...

Finally I would say that the recommended method of learning about all of this and more is to take a course at uni. You should take C programming and operating system architecture where you should learn assembly. Then you should take a course where you get to build you own OS (http://www.uio.no/studier/emner/matnat/ifi/INF3151/index-eng...) followed by a course on multi core architecture (http://www.uio.no/studier/emner/matnat/ifi/INF5063/)

I would recommend not jumping right into x86 and instead starting with something simpler. I learned MIPS in school. The instruction set is very easy to wrap your head around.

MIPS Quick Tutorial: http://logos.cs.uic.edu/366/notes/mips%20quick%20tutorial.ht...

A simulator that will let you run MIPS on windows/linux/mac: http://pages.cs.wisc.edu/~larus/spim.html