Not sure about the most popular set. However, I use a combination of two addons for my water which I find really realistic. First is Waterzone, and over top of that Orik's water enhancements. They can both be found here at simviation.
As for the shorelines, I never really take notice of them, but they are still there for me.
I recently lost my shore waves too. Haven't addressed it yet........ hopefully it is fixable without reinstalling ;). I have not installed anything that SHOULD have affected water textures or effects that I know of.
If your problem is just waves you might want to look at " morwaves2.zip ". It adds 3 sets of waves that are breaking along the shore. For a long time I couldn't run max water effects on my 3 gig machine with a 9800 card. I think the biggest reason for me to be able to run them now is because I turned down my sound acceleration to standard instead of full sound acceleration.
"FS 2004 More Waves II Improved version of alternative coastal breakers with more waves. Balanced to look/move like the surf on shallow waters. No impact on frame rate. By Luiz Alvarenga"