Thats a really tough one :-)
I think its best to sort this out at the time you are shooting it, such as shoot fast handheld (I Know some are going to say, that you will miss the nodal point...but..thats another story) my own experiment is to shoot the next shot when the next wave comes in, at the point where the other was breaking. Its a lot of trail and error here. but if you are wanting higher resolution images, by which I mean shooting multi row, then this is one option that will work OK.
Alternatively is to shoot with more overlap and a wider lens.
Both PTGui and Autopano will give average result here, I often resort to PS for this. In my own case where I also shoot for HDR with 3-5 shot per frames it gets even more difficult! :-)
I would give it a shot in PS CS5 if you have it! but even PS CS4 had a good blender
good luck
Henrik
PS: I need help with correcting perspective on panos! any takers!
