There are a few decent tutorials on this, but I can't find any using Blender 2.5. Still, the principles haven't really changed from 2.4x. Making a realistic water animation is usually done by animating normal, color, and/or displacement maps across a plane. In 2.5, this is done by creating empties and assigning the textures to "object" instead of "generated," choosing empties as the objects, and then animating the empties over the plane. 

This ocean tutorial on this page is rather old, but if you're familiar with the older interface, then you probably won't have much trouble recreating it in 2.5.

http://www.cogfilms.com/tutorials.html