Generally speaking, if you're not going to use linux software RAID with the mdadm tools, I'm not a big fan of RAID controllers integrated on the motherboard. Why not? If the controller dies you're completely out of business--and it may be difficult to obtain another board immediately.
Moreover, many of the onboard RAID solutions aren't actually true hardware RAID devices, and will not work with linux.
Linux software RAID has come a long way over the years--it's definitely a lot better than the Microsoft offerings.
One of the biggest advantages to using it is that, following the proper steps, you actually can physically move the drives to a different server, and then re-mount your data in the new environment, if necessary.
Another advantage of linux software RAID is that you won't need to use a vendor-provided hardware driver for you RAID card--which may not be supported in the near future, or proves to be unreliable in your configuration etc.
The biggest disadvantage to linux software RAID is it's a bit difficult to learn at first--there aren't a lot of pretty graphical tools available for managing it as yet.
If you were to use a hardware RAID solution I probably would suggest one of the offerings from Areca or 3Ware--both have pretty decent linux support and, if this is a mission-critical server as it sounds, you could purchase two of the RAID controllers at the same time, in order to have one available as an immediate replacement.
The RAID controller itself shouldn't be just a plain 32-bit PCI card; for best I/O bandwidth I would aim either for a 64-bit PCI adapter, or one that utilizes PCI Express (PCIe). Obviously you will need to purchase a motherboard that fully supports the slot needed. (Although you can install 64-bit PCI cards in 32-bit slots, they will perform at greatly reduced speed, effectively negating possible performance increases the 64-bit bandwidth otherwise provides).
Motherboards:
While it might be ideal to get a server-class, or at least workstation-class motherboard, as both tend to have designs that include an increased focus on overall I/O throughput, you may do just as well to purchase a decent "desktop"-class board along with a pair of RAID cards (as mentioned above) for about the same price, possibly less.
Most of the more recent desktop boards come with at least one or two extra PCIe slots.
Memory:
Do you need 4GB of RAM? Will you be running a kernel that actually supports the full amount easily? Your CPU of choice, the 6400 X2+, in addition to the standard i386/i686 kernels, also can run the X86-64 kernels, which don't actually have to use the Physical Address Extension hack. It basically means your system will be able to use the full 4GB of RAM more effectively--a definite bonus on servers hosting multiple databases.
If you can afford 4GB, go for it. If you're really limited on funds, though, you might want to purchase just 2GB and focus on upgrading another part of the system.
Hard Drives:
I know you mentioned four 200GB SATA hard drives... but if you have the funds, I would recommend going for four or more of the Western Digital Raptor 160ADFD drives. Sure, they're only 160GB each, but they're also 10,000 rpm enterprise-class drives, and provide great performance in a striped RAID array (0 or 5 etc.). Almost SCSI performance for quite a bit less money. They require decent cooling, though--tend to get a little warm
Hopefully this helps give you some ideas. Sorry if I babbled on a bit.
