There's an interesting post at Freakonomics where economists describe how to protect rhinos from poachers, and specifically whether it's better for donors to give money to the more-needy but more-corrupt Zimbabwe, or less-needy and less-corrupt Botswana. I especially like Emily Oster's answer that you look at the value of each marginal dollar in deciding where you allocate your donations.
Somewhat tangentially, I have my own idea for helping: flood the black markets in rhino ivory, ground-up tiger bone, and all other animal parts with counterfeit versions. This will somewhat depress the value to consumers since they'll be less sure that they're getting the "real" thing, and will decrease their demand. More importantly, the large increase in supply from the counterfeits will decrease the price that "authentic" suppliers can charge. Ultimately, it may help end demand for the animal parts as aphrodisiacs and folk medicines, as people learn that the fakes and the authentic parts have only a placebo value, and that illegal Viagra is much more effective.
Ivory and rhino horn obtained for aesthetic purposes instead of medicine might be a little harder to fake, but not impossible, and the buyer might not care as much either if the item is fake.
It's at least worth some investigation, I think.