Dale, the NEPA process applies to all your examples. Of course the lead agency doesn't have to implement public comments, but they do have to consider them and explain how they were considered in the decision document. For example, when Garry Oye wrote his informal memo implementing the wag bags (which was not an official NEPA decision document), he simple wrote that comments were considered. That doesn't cut it. A decision document is supposed to make a good faith effort to address the comments. Often they bundle the comments into a group or by issue and address them as a group. A Final EIS might have an appendix with all the public comments in it and an explanation of how they were addressed.
As Ken stated, agencies don't usually take Joe Public very seriously. Joe Public is often misinformed or is labeled a NIMBY "Not In My Back Yard." Also, they assume Joe does not usually have the time or resources to follow up with a lawsuit. And let's face it, some agencies will simply do whatever they please unless directed otherwise by a court.
But organized groups are another matter. They tend to have expertise on the matter at hand and resources to fight it out in court. If they are politically connected like the commercial packers, then they have even more clout.
