I recently worked my way through "Programming From the Ground Up" and found it to be a good introduction, but note that it's only x86 (32-bit). You can easily compile and link your code in 32-bit mode, but you'll be working with 32-bit registers and pointers, and some slightly outdated techniques for making syscalls and such. At first I tried translating the book's examples to x64, but found it was pretty painful to mix that task with the complexity of learning assembly.

http://savannah.nongnu.org/projects/pgubook/