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 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