ok, thanks for the answers. I guess I should give a little more details. I work in a research lab. I have a budget of about $13K to spend on this server. We are doing sequencing experiments that will generate ~50GB of data per run and some microscopy experiments generating between 25-50GB of data per run. I'm not entirely sure how many of these experiments will be done and for how long. I initially got a quote for a 16TB array. In that were 16 1TB SAS drives (Seagate ES.2 SAS, 7200 RPM). I've read nothing to suggest that 7200 RPM SAS drives are better than the RE3 drives, so since they are about $60 per drive cheaper that gives me a lot more money to upgrade the CPU and RAM specs. But if I go back to the 16TB solution (which is probably more than enough for some time) and choose 16TB array with RE3 drives in RAID10 (32 drives) and use 2TB drives in RAID6 for the backup that is still almost $1K cheaper than the 2 x 16TB SAS (7200RPM) subsystems, which is money I can use to get faster CPUs. I should also point out that a neighboring lab has a 12TB and a 32TB array completely made of Hitachi 7K1000 (1TB) drives and they have not had any problems with this configuration. Since we aren't "enterprise" class organizations I'm not sure why SAS would be any better.
To answer Chopper's 1st question: the quote I'm looking at says "LSI Dual Port 8880M2 Controller with BBU installed". This would control two identical subsytems (per the quote). Though what I'm describing is two separate but nearly identical sized arrays (would that be a problem?) Another option is a master node with a subsytem (no CPU) for backup. That has a 3Ware 96904i4e controller with BBU installed.
For Chopper's 2nd question, I don't know which OS we will be using yet. Are you saying Windows server 2008 can't handle arrays larger than 16TB? Or just "unsupported" as in no official MS support? I think the vendor uses CentOS for the linux, which I can't stand. We have CentOS on our microscope computer and it's been a pain. I need to first make sure which platform all our applications run on, so far Matlab, R, and the aligners I use run on Linux, so no prob there. I could always install Ubuntu (or Mint, my fave, on it instead).
There are so many configuration options it's enough to make my head spin! Thanks for all your help so far. I hope I can contribute back. This is a helpful website.