This has mainly to do with the number of memory address lanes available to the system, and how the OS uses and addresses the memory itself. But first off - if you have 4GiBytes of Memory in your system, chances are you will see only 3.25GiBytes available.

This is mainly due to the fact, that all PCI/PCI-eX Devices allocate some memory for mapped IO Calls / DMA accesses, and to be able to access this reserved memory in a linear way, you need to be able to talk to these in 32 bit mode - thus the 4GiBytes limit. Note that the missing memory has been mapped by the physical extension cards starting from the upper 4GiByte limit downwards. Means the more memory a card allocates and the more extension cards you have, the more memory will be missing.

Even on 64Bit CPU/OS's combinations you may see this beheavior. Many extension cards still use 32Bit registers. These can only address the first 4GiByte linearly, thus allocate memory from 4GiByte on downwards - recreating the problems due to backwards compatibility.