Assuming you are using seperate drives, one for Windows & applications, the other(s) for video & audio:
On your Windows drive, you should at defrag weekly or so, or as needed. The amount of fragmentation shouldn't be too much if you are accumulating a lot of junk.
On the media drives, its easier to just delete everything on the drive before beginning a new capture. Or if you can't delete everything, delete everything not needed for the project. Defrag the rest, then capture. You could even do a quick format, but don't pick the wrong drive.
But if you have a project running & working, don't mess with it. Finish your tape, etc., then just delete.
I use Disk Keeper as my Defrag application. It is amazing how fragmented a drive becomes after working on a NLE project (especially a big one). I always defrag after completing a project and doing "the housework".
BTW: I recommend Disk Keeper
Shooter Film Company
Disk Keeper is excellent and I highly recommend it as well. Just be careful with external drives such as USB and those in firewire enclosures. On those my version of Disk Keeper seems to think they need to be defragmented every 5-minutes and once it trashed one of my USB drives. On my internal drives, it works flawlessly.
Disk Keeper is also much faster than the Windows defrager, I also used to reformat my drives before starting new projects and stuff, but Disk Keeper defrags so fast, plust SATA drives are fast to begin with -- that although I still do that at times, I don't do it quite as often.
In my opinion, defraging should be done on a Windows PC, don't know why Mac's and Final Cut don't need defraging though. You should have multiple drives as well for NLE, I have a Windows drive, a drive for my DATA, a drive for cache and TMP files and another huge drive for VIDEO. Every so often I format my VIDEO drive entirely and scan thoroughly for disc errors. I also backup with TrueImage and have a few Lacie external drives for project backup. Wish I could get PP2 project manager to trim for archiving but it chokes on most of my complex and longer timelines.