I know that IDE drives were not supported for SQL Server, as there is a function for synchronous writes that SCSI had that IDE did not. I am not sure if there is any update for SATA drives. Not having that direct write capability could lead to a database corruption, if a transaction log write is missed or dropped. This would only happen for a heavy load, I think.
The choice of RAID is usually a balance between cost and performance. RAID 5 gives the most diskspace with some redundancy at the lowest cost (unless you want to give up redundancy, but let's face it. Disks fail). If you need the performance, you should look into either a mirror or a stripe set of mirrors for the data. If you go that far for performance, then you would probably want the separate raid controllers. I am not sure if the servers we get here have independent raid controllers, but I expect they do.
For SQL Server, you will definitely want to favor cores over speed....to a point. Adding cores becomes a diminishing return after a certain point. Fortunately, this point is a little further out for SQL Server, as it is a multithreaded application. Actual number of cores would depend on how many simultaneous queries you expect to have running at any one time. I have boxes with only two cores that are serving up 2 - 400 batches per second with relatively little problem. Naturally, that will depend on what sort of queries you are fielding (on this server, they tend to be simple index seek operations). For a data warehouse that is doing reporting on large data sets, you may want more cores for better parallelism.
Server class memory may also be good to get. There is error checking memory that I have not had to deal with in some time. Head on over to TomsHardware.com, and see if they have any articles about ECC memory.
It has been a while since I put together a machine, so I am not sure which (if either) is better or not. Make sure you schedule a load test or two, to see where your test system starts to choke, so you can make sure the production system has a beefier part in that location.