What Raid to use?
It's faster. RAID-5 offers more disk space but the parity bit messes things up, unless you have some uber hardware-raid card that caches that operation. Personally I am not a fan.
128K - this is really good for INNODB, you'll see a huge boost in responsiveness by making your Stripe Size 128K. I had a 64K stripe size, and I was blown away by the improvement of 128K
mkfs.ext3 -T largefile | mkfs.ext3 -T largefile4
Unless your going to have millions of files, this is a good option.
Make sure /etc/fstab mounts the mysql partition or the data that mysql resides on with noatime.
atime is accesstime: this is a huge boost in performance, tracking each time your ibdata file was last access is worthless, so don't do it.
From other benchmarks that I ran, I think that IBM's open source File system may be better then ext3 for certain workloads. Once I have more information I will post it here.