Why Raid 0?
If your disks are more than one year old, I'd not dare use Raid 0 - it's very risky. If you just need a performance boost from your drives, I'd recommend getting a new bigger 7200 rpm disk with 16 MB buffer at least. Tom's hardware has very interesting interactive hard drive charts
here.
Regarding onboard or dedicated card, it all depends on the specific chipsets featured, and the details of your computer usage. Is the PC going to boot from the Raid array? If so, you must ensure that your flavor of windows supports a repair installation on these disks to make sure you'll be able to fix any potential problems in the future (meaning several tests are needed). Vista and RAID is most likely to guarantee an adventure - test extensively.
If your application or your data are critical, you'll also want to be able to monitor your disks' health, using some SMART monitoring tool. The general lack of the latter in RAID arrays is the main reason I don't use RAID at all. Last time I checked, very few specific chipsets support SMART (e.g. LSI MegaIDE, 3ware PATA/SATA controllers) or offer their own dedicated SMART reading tools, while the monitoring software available generally supports SCSI arrays and not ATA (IDE) ones.
Returning to your original question, I'd start from the onboard controller (which is likely to be more documented and have more recent drivers), make some tests, ensure good airflow on the disks and research on a way to monitor disks' health. And never forget to check periodically for latest updates to your chipset drivers, especially if on Vista.