OK - this one is a little more involved than the other best practices I've posted here. In fact, I'm going to have to send you off to another document at the end of this post to explain the technical background and the exact steps you need to perform, but I still wanted to bring the topic up here for completeness.
This has less to do with setting up or altering SQL Server, because it deals with your initial disk setup. Yes, this has to be done when you're prepping the drives, or you'll have to burn everything down and start it again, so it isn't one of the best practices that you can easily implement after the fact.
At a general level, it has to do with the way the drive geometry is laid out, how the Windows operating system lays down partitions on top of that, and then how SQL Server rides on all those. "Aligning" means making sure the partitions fall within the drive offsets correctly. Like I said, this is kind of involved, but if you read the link at the end and do a little Binging, you'll find what you need.
Why does this matter? Well, we've seen a dramatic - and I really mean dramatic - speed increase possible if the partitions are aligned. Happily, the Windows 2008 Server operating systems have a better method of alignment right out of the box, so if you're on that OS, you have it a little easier. More after the jump: http://msdn.microsoft.com/en-us/library/dd758814.aspx