I have been doing some work with Websphere Application Server this week, prepping a beta install of Lotus Connections 3.0. My Beta environment is Windows 2008 64 Bit. Most of my sandboxes until now have been Windows 2003 32 bit. Not a lot of difference between them, just one small thing you need to be aware of. When you Install WAS during the install you have the option to create a Profile My personal preference is to not install a profile at this time, but rather install WAS and any required fixes, and then come back and use the Profile Management Tool to create the profile I need for that particular instance. This is also helpful if you clone machines and use them for different purposes (ie deployment manager or Application Server). In the 32 Bit version of WAS you can use the Graphical Profile Management (tutorial) tool to create profiles. The Graphical Profile Management tool is not available in the 64 bit versions of Domino (except for Linux on zSeries which I am sure will please Bill) From the WAS 7.0 Infocenter
You cannot use the Profile Management Tool to create profiles for WebSphere Application Server installations on 64-bit architectures except on the Linux for zSeries platform. However, you can use the Profile Management Tool on other 64–bit architectures if you use a WebSphere Application Server 32–bit installation.
I had forgotten about this, so I spent a few puzzled minutes looking for the menu option for the Profile Management tool, when I finally remembered it did not exist for 64 Bit. If you are on a 64 Bit install of WAS you have to use the manageprofiles command located in the<WAS_ROOT>bin directory. You can find the command line options here.