Microsoft employee Eric Law explains in a blog post that there's little advantage to using the 64-bit version and that it suffers from worse JavaScript performance due to the lack of the Just in Time (JIT) script compiler:
Q: What does 64bit IE9 get faster JavaScript benchmark scores than IE8 but slower scores than 32bit IE9?
In IE9 there's one other major difference between the 32bit and 64bit versions of IE. IE9 includes a new script interpreter which is much faster than the script interpreter in IE8. However, 32bit IE9 also includes a Just In Time (JIT) script compiler which converts script into machine code before running it. There is no JIT compiler for 64bit IE. So, for benchmarks like SunSpider (and script-heavy sites) 32bit IE9 runs script up to 4 times as fast as 64bit IE9 (which itself runs script around 5x as fast as IE8). So, you could end up paying a significant speed penalty when using 64bit IE9 vs using the default 32bit version..