Good ones for boot drives--save the four slide trays for RAID.
My long range plan is SSD for my boot and applications, and then RAID SSD for working drives, with a large number of TB drives for redundant external storage. The case on the left is an old G5 case modified to hold up to twenty (20) drives, ten (10) of these in hot swap trays. Theoretically it will hold 40TB of storage. It is served by a Sonnet four port card (last picture).
I'm not sure if external storage to this extreme is really necessary with my latest mod shown below (second, third and fourth pictures), and the continuing growth of storage technology.
So,
the stock Mac Pro can hold 12 drives internally, which would be plenty, or
8 drives if you keep the optical (my choice). The way SSD drive growth is going, I don't see much need for external drives except perhaps for backup.
Apple RAID: My feeling is the Apple RAID card is useless. It doesn't have enough throughput. I'm going with an Areca RAID controller--their fastest is a little more than Apples, but Areca charges extra for battery backup and extra memory. It can serve both internal and external drives. If I had one now it would expand my options nicely.
Windoze: I don't see any point to using bootcamp for Windoze either. Solaris--yes. Linux--perhaps. Windows? I put it on and never use it. Would you drive a Yugo when you have a ZR1? No. In any event, if that is important to you, it is as simple as changing a few cables.
Drives: The SSD drives are almost at the level of performance I'm looking for. I want something like the Nitro TB SSDs--due out later this year. I can fit as many as six SSD's in my Mac Pro--four (4) 3.5" and four (4) 2.5". So I'm thinking one for boot, one for applications, and 4-6 for SSD RAID 0. Or some similar variation--perhaps two (2) RAID 0 for boot, two (2) RAID 0 for apps, and four (4) for working data/scratch.
This is probably in the wrong order, but I'm going to start out with an SSD drive for a boot drive (sata port 5, then one for Applications Sata port 6) stealing ports that used to serve external drives. I'm also looking into converting the IDE cable to Sata and putting a back up boot drive on it in the 2.5" drive cage. That would allow me to serve 3 2.5" drives without adding a hardware RAID controller immediately. Optionally, I am only using two (2) of the four (4) Sonnet ports. I could route cables from outside back into the case and instantly have all four (4) 2.5" drive bays attached. This is a little sloppy looking but it would be a good short term option--and the one I'll most likely take.
Next for me is an Areca hardware RAID. My goal is just under 1200MB/sec in RAID 0, which the top end Areca card will approach--it should easily beat 1000MB/sec. Smoking performance? You bet. How many streams of High Def uncompressed video? I'll guess four streams. The only way to beat this would be to use one of the new Mac Pro's with the same setup.
My idea for a working RAID will be four 500GB (or larger) 3.5" SSD's in harware RAID 0--these aren't being made yet. So for now, I'll get by with four TB drives in software RAID 0 and then hardware RAID 0...
Externally, I have space for 20 sata drives using my four (4) Sonnet ports with port multipliers in the expansion box. No need for speed here. I have over 8TB capacity so far. I'm trying to slim down by purging as many unnecessary files as possible to reduce my dependency on storage space.
Great minds think alike. Someone else talked about putting a cage of 2.5" drives in an optical bay.
Someone else suggested it is not a big deal to slide this cage out to expose the drives. I would not modify the case.
So the reason I found this thread is I'm replacing the cables that I ran externally. I originally bought these to add some external storage. I now have for external sata ports and would rather have these four 2.5" drives working.
So I was looking around trying to decide what type of cables to get to replace my existing port 5 & 6 cables. And debating running my last two external cables inside the case to serve the last two 2.5" drives, or else wait on that and go for the RAID card next.
Those extra Sata port are valuable. And one of these would be my first choice for an OS X boot drive. If you really want to boot windows, then I suggest you make the appropriate cable changes swapping drive bays 2 and 3 with 5 and 6, and run 1, 5, 6, & 4 in hardware RAID. Boot OS X off of 2, and Windows off of 3, unless alternatively, you chose to partition one of these.
My advice is to keep independent disks for your different operating systems. With up to four (4) 2.5" drives run off Sata ports 1-4, and an Areca RAID controller serving the stock drive bays, and perhaps a few of the 2.5" drives--this would be a nice setup and all drives would be easy to swap if necessary.
One more thing. I mentioned the second optical bay's IDE cable. It is possible you could boot windows off of this with the right adapter. I have only found one that might work. I haven't tried it yet, but it is not a bad idea, using up a less important port for a less important operating system. I'm fairly sure it will boot windoze, but I haven't tried it yet, and it won't be a priority for me to play with this idea.