Wow...lots of questions, but here goes.
performance wise would it make sense to split the sata mirror into two partitions, one for OS and the other for important data and then use the IDE drives for applications
Yes, if you install the OS & apps to a smaller partition (this depends on how big your OS & application use is...look at your current WINDOWS & Program Files folder, double them, then add 10 gigs) the OS & apps stay to the outside of the platters and will load faster than if a drive head has to dance over 250 GB of data to find what it needs.
If Vista Ultimate offers striping/mirroring would it be a good or bad idea to implement that with the IDE drives?
Yes, it would be a bad idea. Since you are most likely using hardware RAID controllers on your mainboard (you should post the model# in your question) for the 250GB drives it is ALWAYS a bad idea to mix hardware & software RAID. Vista may have smoothed this out but I'm not willing to gamble on it, are you?
Would there be a benefit to putting the hard drives on separate controllers with one sharing with the optical?
Yes. Put drive #1 on IDE1 as master and drive #2 on IDE2 as master with the IDE optical as slave on the secondary.
My personal recommendation would be to create a RAID 1 array with the new 250GB drives, then partition the array into 50GB/200GB partitions. Now you have a redundant installation which will cover you if one of the new drives fail.
I would then partition one of the IDE drives into a 50/150 drive. Using NTBackup or Acronis, I would then set up a backup schedule for the data array to auto-backup to drive #1 (full 200GB), and the OS & Apps to the 50GB partition. This leaves another 200 GB for your "unimportant" files.
NOTE: If you are a performance-over-safety freak, you can instead build a RAID 0 array with the two 250GB drivs. partitioned into 100/400, and use the two 200GB drives for data-only backup.
As a rule, RAID arrays are constructed in the BIOS before loading Windows. For the sake of clarity I would install just the two SATA drives during Windows install, and connect the IDE drives later. In my case, Vista Ultimate saw my array without me adding drivers (the traditional F6 of XP) so that was all good.
Another reminder, avoid JBOD (or drive spanning) as this might place portions of files on both disks and if one disk goes so does the file. Best of luck.
Tony
"...an eye for an eye leaves everybody blind" - M.L. King