So you just bought and assembled a brand-new AMD64 workstation. The only decision that remains is whether to install a 64-bit Linux distribution, or stick with comfortable, tried-and-true IA-32. If you are seeking an easy answer to that question, I can't help you. Running 64-bit Linux has its pros and cons. Unfortunately, a lot of the cons are out of your hands -- but they're not really Linux's fault, either.
For starters, you should know that there are essentially no proprietary applications for a 64-bit Linux desktop. Google, Adobe, iD, Skype, and the rest of the independent software vendors (ISV) who release Linux binaries of their apps by and large do so solely for 32-bit Intel architecture only.