Partition Alignment, in a nutshell, is making sure your partitions start on Sector # 2048 (or some multiple of 512) instead of the standard Sector # 63.
There are some great blog entries that define the issue, so I won't get into it here.
While you don't need to do this for 2008 partitions (they start properly aligned), I've always known I should align my older 2003 partitions, but I haven't bothered. Today I decided to do a simple test to see the results of running un-aligned.
Test Details:
OS: Windows 2003 32bit
Test Package: Performance Test 6.1, running Webserver disk role benchmark
VM: ESXi 4.1
Drives: NFS share to a Solaris 11 ZFS box.
I chose the webserver role because it's a heavy reader (writes are harder to benchmark on ZFS), and because it's my worst performer. The other roles are hitting 900-1200 MB/sec, which is close to the max I can drive through my 10Gbe card.
Aligned Partition: 609 MB/sec
Non-Aligned Partition: 436 MB/sec
That's a 30% increase in read speed. Wow, that's a lot of speed to throw away for not aligning a partition.
Here's a link to a quick little tool that will let you know within Windows if your partition is aligned: http://ctxadmtools.musumeci.com.ar/VMCheckAlign/VMCheckAlignment10.html
Of course, it can be a pain in the ass to align a partition. You can use a livecd of gparted, or create a new disk and partition it with Windows 2008, copying the data to the new partition from a seperate VM.
Some partition tools are now including the ability to quickly and easily specify a aligned-partition start, so hopefully this will be an easy task in the near future. If you know the name of any easy booting GUI type partition tools that can move a Windows partition to sector 2048 without much fuss, please let me know and I'll post it here.
I personally do it with gparted live, but I'm also not affraid of the command line. Something easier would be nice.