I've recently encountered two sets of very useful books on PC architecture. To work on the bare iron there are about a gazillion books you would need, but the following book provides an excellent leg up:
The Indispensible PC Hardware Book, Hans-Peter Messmer, Addison-Wesley (mine is second edition)
It includes a detailed discussion of all of the various versions of the PC, and some details on using the ports and/or the bios to program them. The combination of technical overview plus historical perspective is especially valuable, as compatible software needs to take all of this into account.
I've also been impressed by the Mindshare Press series of books on PC architecture. These are not all-in-one, and are more electrically oriented than programmer oriented, but are worth having nonetheless.
Jonathan