What is the difference (use, effectiveness, etc.) between aciphex (rabeprazole) and prilosec?

Very similar. They are both from the same class of medications so very similar, though people can always reposed differently to medications. Prilosec is available over the counter as well.
Medications. They are comparable medications in the same family of medications referred to as ppis. Major difference is the effect for relief of symptoms in a particular patient. Either drug may or may not be effective for relief of symptoms due to acid reflux("heartburn") or ulcer type symptoms. It is not uncommon for a physician to use different ppis until finding the one which provides the best relief.