If you're looking for organizations that make a difference, I've complied a list of some of the ones I like the most below. Keep in mind, there are also citizen science projects you can get involved in to make a difference and many little every-day things, like taking shorter showers, knowing where your products come from and how they're produced, and more ex-situ conservation steps that all have an impact.
Born Free Foundation is a UK-based organization that protects wildlife around the world. Investigating the impact of tourism on polar bears, supporting the UN Great Ape Survival Project, and fighting the ivory trade are just some of their projects.
The Center Biological Diversity seeks to protect all species facing extinction. They work with public policy, raise awareness of human consumption, and protect species from global warming.
Conservation International has been working for over twenty-five years to protect the planet and its
biodiversity, understanding that humans rely on Earth.
Durrell Wildlife Conservation Trust is a UK based organization that works to protect vulnerable species and ecosystems, offers volunteer opportunities abroad and in the UK, and they also offer courses through Durrell Academy. They've recently launched the Durrell Index, which tracks their progress and measures how they're making a difference.
Fauna and Flora International is a nonprofit conserving species and ecosystems in over forty countries. Since 1903, they've worked to create scientifically-based conservation solutions that take into account human needs.
The International Fund for Animal Welfare helps domesticated and wild animals, working in political advocacy, wildlife trafficking and education.
Natural Resources Defense Council seeks to protect the people, plants, animals and natural systems on which we all depend. It takes on many causes, such as clean energy, commercial whaling, plastic pollution in our waters, toxic pesticides, grizzly bears, and much more.
WildAid works with many different types of species with the purpose of ending the illegal wildlife trade. They work to protect tigers, sharks and other animals. They also have an environmental program in China and work to protect our oceans. Charity Navigator named them the number one wildlife conservation charity of 2014!
Regional or Ecosystem Specific
Conservation Northwest focuses on the NW of Canada and the US, protecting wildlife habitat, protecting old growth forests, connecting habitats for wildlife, and more.
Mission Blue is a community of multiple organizations answering a call to raise awareness about ocean issues and inspire support to tackle these issues and scientific pursuits to make a difference.
The Polar Conservation Organisation works to raise awareness and education people about the need to protect the the polar regions.
The Rainforest Action Network campaigns for the forests through education, grassroots and non-violent action.
The Wildlands Network operates in North America and seeks to protect wildlife and wild places for future generations.
Primate SpecificApe Action Africa address the immediate threats to chimpanzees and gorillas in Cameroon. They help orphaned apes and reintroduce them to the wild when they're ready, run education programs, and help determine areas that should be set aside for conservation purposes.
Gorilla Doctors is a team of international vets committed to helping mountain gorillas and Grauer's gorillas. They regularly monitor the health of gorillas and intervene to aid injured animals or orphaned gorillas.
Formed in 2009, Primate Connections links multiple primate grassroots organizations together with each other and the public. They also produce a calendar which features these organizations and which the proceeds go directly towards primate conservation and education.