With the advent of Advanced Format drives and their new 4K low-level sectoring scheme a new, performance-robbing phenomenon known as misaligned partitions has shown up. Paragon Software's $30 Paragon Alignment Tool 3.0 fixes the issue, albeit slowly. However, you probably don't need it. Both Hitachi and Western Digital provide alignment tools for their drives, and Seagate claims their SmartAlign technology obviates the need for tools.
The partition misalignment issue is the result of legacy operating systems which use 512 byte sector schemes and AF drives which use 4096 byte sectors. Under some conditions the two schemes will misalign, causing multiple accesses where one would be sufficient. This occurs only when you restore images of older partitions to an advanced format drive, or partition an advanced format drive using XP. Aligning misaligned partitions can greatly increase performance--up to 30% according to PCWorld's recent tests.
Paragon Alignment Tool's Windows interface is simple and straightforward. Its purpose is to tell you whether your partitions are misaligned and ask you what to do about it. Those on my boot SSD were fine (SSDs are not affected by the legacy alignment issues), but those on my mostly full 1TB data drive were misaligned so I had a good chance to test the program. It worked--mostly. It aligned all the partitions except one, the first on the drive due to errors. Make sure to check your partitions before running the tool.
Beware using Paragon Alignment Tool during working hours. I made that mistake, and was kicked off the computer for a whopping 10 hours. Every bit of data must be shifted, which can take a very long time. The alignment process is performed after a reboot, before entering Windows, so you can't work while it runs. Sadly, in my case the program didn't recognize my keyboard (a PS/2 unit attached to a USB converter) so I couldn't abort the process. There were also odd flashing graphics and the only portion of the display that tracked true was the progress bars. The actual amount of data copied or the rate never showed up.
In the morning I returned to find that the program had finished, albeit with the one partition still not aligned. It worked for the most part, and for the most part was forgiven. The Partition Alignment Tool includes a Linux-based boot CD for operation on systems without operating systems. The big question is, why pay when the drive manufacturers provide a free alternative?