The 6-9mo thing is just what is recommended with a computer. Any user realizes that just over time lots of stuff (software) gets installed on a machine and bogs it down. Formatting and starting fresh again allows you to remove all that stuff. After all not every uninstall program removes everything, the registry gets loaded with excess information, and often you have patched patches (in MS and Apple terms). If you have never done in when you format your machine and start installing software you will be amazed at how much faster everything runs. Plus when you download patches you will have the newest version. For example you may have install Win2k, downloaded SP1 then later SP2....however on a fresh install you would just download SP2 now and patch it (since it has all the SP1 info and more in it). This is just a good rule of thumb to start fresh every 6-9mo. Depending on how heavily I am using my workstation depends on how often I re-do the machine. During heavy usage I re-do it about every 6mo. Lately I've been using other machines so my workstation gets re-done every 9mo.
Another when I first starting working as a Computer Techie (around 6 years ago) I learned a very valuable piece of information; Never upgrade an OS (Solaris and some Unix varieties may be the exception but as far as Windows or Mac this applies). This is the same principle as patching a patch.
If you are working with Windows 2000 I'd recommend following tutorials on integrating a service pack into the Windows 2000 install CD. This allows you to do an install from the CD with SP2 already installed. I've seen this fix many problems that SP2 caused when added to an existing install (most of these seem to be w/ Wildcat cards). An example tutorial is here; Making a Bootable Windows 2000 CD with Service Pack Integrated.
I've been administering 3d workstations at two different locations and these techniques have always served me well there and on my home machines as well.
Feel free to drop me more specific questions. It is hard to pour out the brain all at once on this