One of the so-called "nice" new features of Windows Vista is the "rebuilt" defrag engine. Problem is, I don't like it. Why? I like to SEE what's being defragged, and I like to SEE a visual representation of what my filesystem looks like.
The main reason for this is that I can choose different defrag methods (such as with O&O Defrag) and get better file ordering. Also, when I get to see what's happening, it helps me to identify files I know I don't need and I can delete them, and do a follow-up defrag.
Unfortunately, O&O doesn't have anything out for Vista yet (yes I know you can Orca the MSI, but I ain't doing that!). Diskeeper isn't ready for Vista either.
Frankly, I don't know what these people have been doing all this time. They knew Windows Vista was coming out, the defrag API has been readily available to them to get their products ready. What, were they waiting for Godot?
At any rate, Raxco, which makes PerfectDisk, has a free 150 day trial of their Vista-compatible beta, and it works great. Also, Auslogic has a free defrag that is Vista compatible, but it doesn't offer control of defrag method or offer boot-time defragmentation.
Suggestion: Delete your Paging file before defragging (requires a reboot, and don't forget to press the "SET" button). You can then do the boot-time defrag, which takes care of your MFT and System files, and have a nice fast hard drive. Then, go back to Control Panel / System and restore your Paging file.
Always run the Disk Cleanup Wizard before defragging, and get rid of unwanted .tmp and .bak files.