I read on one of the posts at NRO that readers have inquired about private aid to Honduras now that our President and the State Department have decided that they are to be punished for following their own [democratic] constitution. I'm going to continue to research this, but I went to my old stand-by, Episcopal Relief & Development. They operate all over the world and have a good record of effective aid and low overhead. But, they don't allow donations to benefit a specific country unless there is a catastrophe that needs to be addressed (a hurricane hit Honduras a number of years ago and they set up an emergency fund then, for example.)
Aside: This is a pet peeve of mine and the Episcopal Church is especially good at feeding this particular peeve. Take a look at this page. Notice the quote from Lao Tsu, the Chinese (and pagan) philosopher, who offers a very nice idea about how to help poor people. Would it kill Episcopalians to acknowledge that they are Christian and doing what Christ commanded? Jesus said some pretty cool things on that subject, too. End aside.
However, by startling coincidence, a young man to whom I'm closely related, is a member of Engineers Without Borders, and they have many, many projects down in Honduras, most in developing safe water sources. You can donate to a specific project (pick a school- I don't think it matters, but I'll go with University of Missouri Science & Technology). I'll get more information about these projects and their financial needs, but safe drinking water is fundamental. You can't go wrong helping people in this way.