If you have the time to learn it, I would recommend using Solaris because of its ZFS file system. ZFS is designed for data storage in mind across a large number of drives. (Here is a link with more information http://www.sun.com/software/solaris/ds/zfs.jsp) Unfortunately Solaris does cost money($1000/socket) and their is no real good free edition any more seeing as opensolaris is no longer being released. You can however download it to test and try out or use for development, you just need a license for production use. There are open source versions of solaris but most of them are not ready for any real use.
If you don't want to work with Solaris then go with linux. I would recommend Redhat Enterprise if you want support or the free version Cent OS. Unfortunately their is no stable version of zfs for linux so another file system would have to be used.
From what I understand a lot of work has gone into fixing this issue over the past few years. Fragmentation tends to be an issues with lots of copy-on-writes on files that change consistently. hostnmail said that the usage would include a lot of backup and archives and other large files so I would imagine that fragmentation would not be all that much of a problem.
At some point there will be a defragmentation utility tool that would fix this issue completely.
2x 3ware9550SX-12 Controller
1x 4U 24 bays hotswap case
You might consider using a chassis with an expander backplane (e.g. Supermicro SC846E1-R900B) so that you only need 1 RAID controller and 1 cable. An Adaptec 5405 could handle all 24 drives with a single SFF-8087 cable.