I'm not a big fan of IDE Raid but I'll feild this question and try to give you some pros and cons. I'm sure someoen will correct me if I'm wrong. Just a reminder there is disk mirroring, disk striping, and combinations of the two (at least for cheap IDE controllers).
For striping, you will be "combining" two hard drives to act as one. Spreading data evenly accross the two (or more) drives. This new drive size is double the size of the smallest drive in the array. This will provide a better transfer (with striping) due to pulling data off of both drives simultenously. This does not help with seek time.
This is great for computers that are accessing large files constantly like editing video files and databases. Won't help you load that little text file any faster. Also, this doubles the odds of a hard drive failure wiping everything out (only half the file is left on the undamaged drive).
Mirroring will make an exact copy of your drive and in the event of a failure of a drive, you simply pull it out of the array and move on with a complete copy of your files.
There are combinations of the two that require more drives in the array.
With the exception of one IDE Raid controller (and SCSI raid), they are all a software based version of Raid. THere is no processor onboard that is dedicated solely to the location of the files like on the SCSI Raid controllers. So there will be some CPU overhead.
Decide what is better for you. Sometimes, Raid can be a fickle thing. My suggestion: If the Raid controller is only a few bucks more, get it. You can use it as a regular IDE controller until you want/need to do Raid. Matching hard drives are better for stability but aren't required to give good stability to the array.
I have a Raid enabled motherbaord but do not use it as in that capacity. I use the extra channels but not with Raid. Reason: I have had 3 hard drive failures for one reason or another in the last 2 years on various boards and systems. I don't want to push my luck and double my odds for another. Plus I do not do much that would require the higher transfer rates at the cost of CPU cycles.