It depends....
There is no right answer a best system. It all depends on so many different factors. The move to "commodity boxes" is driven by the same numpties that drove the Dot.com bubble, working in lots of industries, they all seem to be jumping on the Linux bandwagon away from the big-iron, without really considering the whole picture and consequences.
Yep the X64 boxes are way cheaper than the RISC ones but what about the lack of features for partioning, virtualisation at the hardware and OS level that just isn't in Linux or X64 (or Windows)
You have to consider where the business is now and where it needs to be in the next 3 years, balancing the hardware, licensing, performance and human costs.
I moved a major operation from RISC to X64, because in 2006, the latter was so much faster. A major business model
Old RISC: 4h:45
New RISC 3h:15
X64 (AMD) 1h:20
but by mid 2010 I was recommending the move back to RISC as the workload and bandwidth required, X64 couldn't cope. Luckily the business was using an OS that ran on RISC and X64, no new skills or data.
However a year later, the with the arrival of the E7, the rise of flash storage, the prevelence of integrated 10GbE, 8GbFC etc....................... tough call.
Given that the business has a lack of human resources, I'd still stick with big RISC iron as less boxes is best for them and it doesn't make an iota of difference on licensing between the cores.
The big challenge with X64 now is the sheer amount of cores, how do you partition a large box - Vmware and Xen have an overhead but also limit on resources per guest. Linux is very immature, though RH6 is starting to get some decent features that the big boys (AIX, Solaris, Tru64, HPUX etc) have had for years.