From Wikipedia
* Some operating systems reserve portions of process address space for OS use, effectively reducing the total address space available for mapping memory for user programs. For instance, Windows XP DLLs and userland OS components are mapped into each process's address space, leaving only 2 to 3.8 GB (depending on the settings) address space available, even if the computer has 4 GB of RAM. This restriction is not present in 64-bit operating systems.
(This also applies to computers running Windows Vista with Service Pack 1 as it only shows the installed RAM not the usable.)
* Memory-mapped files are becoming more difficult to implement in 32-bit architectures, especially due to the introduction of relatively cheap recordable DVD technology. A 4 GB file is no longer uncommon, and such large files cannot be memory mapped easily to 32-bit architectures; only a region of the file can be mapped into the address space, and to access such a file by memory mapping, those regions will have to be mapped into and out of the address space as needed. This is a problem, as memory mapping remains one of the most efficient disk-to-memory methods, when properly implemented by the OS.
* Some programs such as data encryption software can benefit greatly from 64-bit registers (if the software is 64-bit compiled) and effectively execute 3 to 5 times faster on 64-bit than on 32-bit.
The main disadvantage of 64-bit architectures is that relative to 32-bit architectures the same data occupies more space in memory (due to swollen pointers and possibly other types and alignment padding). This increases the memory requirements of a given process and can have implications for efficient processor cache utilization. Maintaining a partial 32-bit model is one way to handle this and is in general reasonably effective. In fact, the highly performance-oriented z/OS operating system takes this approach currently, requiring program code to reside in any number of 32-bit address spaces while data objects can (optionally) reside in 64-bit regions.
Currently, most commercial x86 software is compiled into 32-bit code, not 64-bit code, so it does not take advantage of the larger 64-bit address space or wider 64-bit registers and data paths on x86 processors, or the additional registers in 64-bit mode. However, users of most RISC platforms, and users of free or open source operating systems (where the source code is available for recompiling with a 64-bit compiler) have been able to use exclusive 64-bit computing environments for years. Not all such applications require a large address space nor manipulate 64-bit data items, so they wouldn't benefit from the larger address space or wider registers and data paths. The main advantage to 64-bit versions of such applications is the ability to access more registers in the x86-64 architecture.
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