Protected Mode and Long Mode 

Protected Mode was first introduced in Intel 80286, providing mechanism protecting resource and assisting multi-task OS such as UNIX, OS/2 and so forth, and enhanced in Intel 80386 processor by extending computing capability to 32 bits from 16 bits, eventually becomes part of IA-32 architecture. Most x86 OS only running within protectected mode such as Windows NT, Linux, and so many BSD distros; but MS-DOS working under real mode, some extender might switch through and back from protected mode for extending physical memory addressing, likewise, Windows 3.x also transit itself from real mode and protected mode thorugh and ack too. Windows 9x not only depends the real mode as bootstrap, but also sits itself from and to that mode. 

Long Mode is a kind of protected mode, not a real mode, but does not belong to the Protected Mode in IA-32, switches itself out of IA-32 dominated Legacy Mode, to a completely self-contained mode, which means even though a x64 processor eliminates its legacy part, it would be fulfunctioned. From the aspect of implementation, or Microarchitecture level, the legacy mode codes could share the same physical execution resources designed for the x64 codes, without needing additional physical execution units for itself, like it found in early Itanium processor. So IA-32 architecture might or might not have relationship with x86-64, x64, AMD64 or Intel64. 

 IA32e and AMD64 

AMD64 is a switched-out architecture from IA-32, providing compatibility mode to support most IA-32 software and representing itself in the Long Mode within AMD64 processors. It is a new architecture, even though most lying on IA-32 architecture. 

IA32e is not a mode, but an extention of IA-32, or newer revision of IA-32, introducing 64-bit computing capability for its fundemental architecture. Intel EM64T is the new brought feature to this kind of processors, enabling it for 64-bit computing. Of course, EM64T is not a mode too, but a feature like PAE, could be enabled to extend the 64-bit computing capability. Without EM64T enabled, Yamhill processor would act like a tradtional Pentium 4. 

After EM64T enabled, 64-bit registers would be visible to applications. 32-bit traditional OS might need minor fixes to support applications referring 64-bit registers to do the 64-bit computings, but programmers must take care of the computing results without intervented by other processes. But most likely as it in PAE, OS might need a patch to support this feature totally, at least to manage the extended descriptors and extended 64-bit registers and stacks and so forth, but without needing to compile the OS from the scratch like it in AMD64. Virtual Address might be extended up to 52 bits, while physical address up to 46 bits. 16K segments of 4GiB could be spreaded to 64TiB physical space, with or without paging. Because the difference between 32bit and 64bit computing is bit width of register rather than the whole system, so 32-bit and 64-bit codes is also differentiated by the referenced resgistered without needing a submode, such as compatibility mode to support tradtional 32-bit software. 

After EM64T disabled, Yamhill processor would act like a Northwood Pentium 4.