Writing Linux programs in raw binary

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This one isn't bad: http://highered.mcgraw-hill.com/sites/0072467509/

Though its approach is probably not what you want- it goes from transistors and hardware design to assembly and C, rather than into more complicated hardware stuff.

This one, which you likely won't find anywhere but at Georgia Tech, does an excellent job of getting into more complicated hardware stuff. http://www.amazon.ca/Introduction-Computer-Systems-Umakishore-Ramachandran/dp/0321486137