For more detailed information on RAID levels you can visit The PC Guide Single RAID Levels and Multiple (Nested) RAID Levels. There is also a HUGE RAID glossary on the Adaptec website that I would recommend looking over as well. The Adaptec site also has a decent section on the difference between Hardware and Software RAID designs. http://www.viaarena.com/?PageID=80
There is no "best" stripe size. Selecting the proper stripe size is all about what you intend to use the machine for. Smaller stripe sizes are good for general day-to-day usage and can help the OS and most programs feel faster. Larger stripe sizes are better for reading or writing very large datafiles, like in the case of editiing digital video or audio.
I would say that 16k or 64k is ideal for a gaming machine. Anything above that is probably a bit too big. Of course, stripe size performance is also affected by the drives you're using, as well as the RAID controller, so there are no absolutes.
You'd have to do it from another hard drive, booted in Windows. If you format frin floppy, it will give you the default 4K cluster size. Not a problem for me, since I have a ghost IDE drive for backup, but a royal pain in the ass for people who don't.
I have 64 stripe size and 64k cluster size with two 36gb raptors, and after a defrag(before the defrag it's MUCH MUCH worse) I get around 75 mb/s write and 50 mb/s read. When I installed XP onto the stripe a couple months ago it was like 90/85, I don't know what happened :-[ I have to defrag extremely often to maintain these meager rates, too. I have two partitions, each score almost the same.
I'm about to reformat with 32k stripe size and 32k cluster size to see if that helps.
But that guy had 95 mb/s average with the same access time as me with 512k cluster and 16kb stripe size. I want to try this configuration, any objections?
edit: using huge cluster sizes didn't help my speeds any, the main thing was using the 16k stripe size. I get around 90 mb/s read average in HDtach now, no matter what cluster size. I'm going to use 32k just for kicks.