When building my own equipment, I am a huge fan of 3ware RAID controllers. This is because they come with an excellent warranty, are cross-platform compatible, and have the best track record of keeping your data intact. Unfortunately, they are the most expensive.
When purchasing equipment premade, I use Dell. Dell configures all of their equipment with SPARC controllers, which are decent and can fit within a lower budget. I am not sure if you can directly order SPARC controllers or if you have to be an OEM.
The type of card you buy is really going to ultimately depend on your computer build. Tower server vs. rackmount server. 1U vs 2U. Hotswappable or not. If you are not really sure what you are doing, I would consider taking a look over at www.siliconmechanics.com and custom building your server via their web tool. Depending on what you want to do, their website will let you configure different builds with various RAID controllers from different manufacturers.
Edit - here is a Xeon server which should be a good starting point for deciding on your RAID controller. (Select the PCI expansion drop downs for the RAID controller options). http://www.siliconmechanics.com/i22738/dual-xeon-server.php
Something to consider, regardless of RAID controller: I would use Western Digital drives over Seagate right now, as the past year has been full of issues with Seagates drives regarding RAID operations. Also, make sure you order "enterprise" drives, not "desktop".
Thanks for the answer - it provided the information I needed. I can build a non-RAID tower for about 30% of what Silicon Mechanics wants for a RAID server, so I will probably go that route. The RAID controller from 3ware would be the most expensive component of the entire solution and if I go non-RAID I don't have to worry about driver configuration and disk size. – jnoss – 2009-12-31T16:58:06.073