I have had GERD for several years now, treated with PPIs combined with zantac. GI doctor explained to me once upon a time that acid reflux does most of its damage at night when I lay down; he didn't really explain what kind of damage, though. I recently visited a pulmonologist, who told me that my chronic cough is most likely related to GERD, and that if acid routinely aspirates to the lungs, it can cause interstitial lung disease. This is not something you want to have, as it normally has a fairly poor prognosis. It seems to me that if PPIs and OTC medications (e.g., zantac) don't completely take care of the reflux, then the nissen fundoplication surgery is the next best option. If my lungs, through future testing, show evidence of reflux damage, surgery is something I will actively pursue with my doctors.
A couple of strategies that have helped me in the past with nighttime reflux: I always take 300 mg of zantac before going to bed; this usually takes care of residual acid after the PPIs (which I take in the morning) have done their job. When I was first dx with GERD, GI doctor started me on reglan twice a day before meals. Reglan, I guess, acts a lot like propulsid (if some of you have been on that drug), but does not have the same potentially severe side effects as propulsid. Reglan forces the LES to contract correctly, thus preventing acid from traveling up the esophagus. I found it to be a very helpful drug.
One thing I've found in my personal research on acid reflux and lung disease is that acid does not always aspirate to the lungs via the esophagus. It can also "cross-over" lower in the GI tract somewhere. Hence, you can be aspirating and not know it. Not sure how they test for this.