Segmentation registers use

1. You must have read some really old books because nobody program for real-mode anymore ;-) In real-mode, you can get the physical address of a memory access with phyical address = segment register * 0x10 + offset, the offset being a value inside one of the general-purpose registers. Because these registers are 16 bit wide, a segment will be 64kb long and there is nothing you can do about its size, just because there is no attribute! With the * 0x10 multiplication, 1mb of memory become available, but there are overlapping combinations depending on what you put in the segment registers and the address register. I haven't compiled any code for real-mode, but I think it's upto the OS to setup the segment registers during the the binary loading, just like a loader would allocate some pages when loading an ELF binary. However I do have compiled bare-metal kernel code, and I had to setup these registers by myself.

2. Four segments are mandatory in the flat model because of architecture constraints. In protected-mode the segment registers no more contains the segment base address, but a segment selector which is basically an offset into the GDT. Depending on the value of the segment selector, the CPU will be in a given level of privilege, this is the CPL (Current Privilege Level). The segment selector points to a segment descriptor which has a DPL (Descriptor Privilege Level), which is eventually the CPL if the segment register is filled with with this selector (at least true for the code-segment selector). Therefore you need at least a pair of segment selectors to differentiate the kernel from the userland. Moreover, segments are either code segment or data segment, so you eventually end up with four segment descriptors in the GDT.

3. I don't have any example of serious OS which make any use of segmentation, just because segmentation is still present for backward compliancy. Using the flat model approach is nothing but a mean to get rid of it. Anyway, you're right, paging is way more efficient and versatile, and available on almost all architecture (the concepts at least). I can't explain here paging internals, but all the information you need to know are inside the excellent Intel man: Intel® 64 and IA-32 Architectures Software Developer’s Manual Volume 3A: System Programming Guide, Part 1

Expanding on Benoit's answer to question 3...

The division of programs into logical parts such as code, constant data, modifiable data and stack is done by different agents at different points in time.

First, your compiler (and linker) creates executable files where this division is specified. If you look at a number of executable file formats (PE, ELF, etc), you'll see that they support some kind of sections or segments or whatever you want to call it. Besides addresses and sizes and locations within the file, those sections bear attributes telling the OS the purpose of these sections, e.g. this section contains code (and here's the entry point), this - initialized constant data, that - uninitialized data (typically not taking space in the file), here's something about the stack, over there is the list of dependencies (e.g. DLLs), etc.

Next, when the OS starts executing the program, it parses the file to see how much memory the program needs, where and what memory protection is needed for every section. The latter is commonly done via page tables. The code pages are marked as executable and read-only, the constant data pages are marked as not executable and read-only, other data pages (including those of the stack) are marked as not executable and read-write. This is how it ought to be normally.

Often times programs need read-write and, at the same time, executable regions for dynamically generated code or just to be able to modify the existing code. The combined RWX access can be either specified in the executable file or requested at run time.

There can be other special pages such as guard pages for dynamic stack expansion, they're placed next to the stack pages. For example, your program starts with enough pages allocated for a 64KB stack and then when the program tries to access beyond that point, the OS intercepts access to those guard pages, allocates more pages for the stack (up to the maximum supported size) and moves the guard pages further. These pages don't need to be specified in the executable file, the OS can handle them on its own. The file should only specify the stack size(s) and perhaps the location.

If there's no hardware or code in the OS to distinguish code memory from data memory or to enforce memory access rights, the division is very formal. 16-bit real-mode DOS programs (COM and EXE) didn't have code, data and stack segments marked in some special way. COM programs had everything in one common 64KB segment and they started with IP=0x100 and SP=0xFFxx and the order of code and data could be arbitrary inside, they could intertwine practically freely. DOS EXE files only specified the starting CS:IP and SS:SP locations and beyond that the code, data and stack segments were indistinguishable to DOS. All it needed to do was load the file, perform relocation (for EXEs only), set up the PSP (Program Segment Prefix, containing the command line parameter and some other control info), load SS:SP and CS:IP. It could not protect memory because memory protection isn't available in the real address mode, and so the 16-bit DOS executable formats were very simple.