x86-64 Resources

Note that this architecture goes under many different names, including "AMD64" and "Intel 64". (But "IA-64" refers to a different architecture altogether, the Intel Itanium.)
Warning: There are two assembler syntaxes in common use for the x86. So-called AT&T syntax, used by the GNU assembler, uses the format "opcode src,dst" whereas so-called Intel syntax, used by Microsoft's MASM assmebler, uses the format "opcode dst,src". When trying to decode documentation, make sure you know which format is being used!

Brief notes on x86-64 programming.
The book by Bryant and O'Hallaron, Computer Systems: A Programmer's Perspective 2nd ed., Ch. 3, has a very useful introduction to the x86 architecture from the perspective of an application programmer or a compiler writer. It covers both 32 and 64-bit versions.
Bryant and O'Hallaron's treatment of floating point programming using the %xmm registers is available on-line in this web aside.
The first edition of Bryant and O'Hallaron covers only 32-bit x86, but a draft of the 2nd edition material on 64-bit programming is available here: x86-64 Machine Level Programming. (Note: there are a few small bugs in this draft. The brief notes are more authoritative.)
A Wikibook on x86 assembly. Google will find you dozens of other web-based resources.
GNU Assembler (as) manual.
A quick guide to debugging assembly code in GDB (pdf)
GNU Debugger (gdb) manual
Official Intel Architecture Manuals for x86.
Official Application Binary Interface (ABI) specification for AMD64 architecture (adopted by linux, but not by Microsoft)