The literature on Yellowstone and the region is rich and deep. There is no way to represent the thousands of science articles, books, and films on the region. I have organized the resources below to include large holdings of materials, some of the most important books on the region, and some high quality general articles for each chapter. Please keep in mind that finding the most up to date articles is still probably faster and easier on Goggle Scholar. This page will be updated periodically.
Yellowstone Science. Yellowstone Science is a Park Service publication that covers the Park's natural and cultural resources using research articles, conference reports, or other special events in the Greater Yellowstone Ecosystem. The entire collection since 1992 is on this site available for download. You can also purchase a subscription.
Holding Institutions
Yellowstone Heritage and Research Center. This is Yellowstone National Park's archive for videos, science papers, books, film and just about anything else related to the park. The entire center is in a newly completed building in Gardiner, MT. A good deal of the materials held are not yet cataloged but the staff is very helpful. 
Yellowstone Research Library. Located on the first floor of the Heritage Center, the library houses a comprehensive collection of printed materials. Most are searchable. For in person visits appointments are strongly recommended.
MSU Special Collections for Yellowstone. The MSU Library has a good collection of mostly historical materials related to the people and history of the region. It is searchable but not up to date and not very user friendly for those off campus. MSU and the nearby Museum of the Rockies both have good photo archives of the region.
Articles and Papers Relating to Yellowstone National Park. This is exactly what is says. This link is a subset on the MSU Special Collections.
Greater Yellowstone Bibliography, University of Wyoming. The archives here are bit hard to sort through but are historically one of the largest in the region. It does not seem to be updated on a regular basis.

Books on Yellowstone. I have no idea how many books have been written about the park and region but here are a few of my favorites, some with a more academic emphasis:
Knowing Yellowstone: Science in America's First National Park - of course I have to put this in.
The Greater Yellowstone Ecosystem. Robert Keiter and Mark Boyce. This is a collection of science and policy chapters organized from a conference that took place in 1989 at the University of Wyoming. Many of the chapters are still very relevant today. This is a book worth reading.
Decade of the Wolf: Returning the Wild to Yellowstone. Doug Smith and Gary Ferguson. This is the definitive book on the reintroduction and the decade after. Heavy on the stories of individual wolves and packs. If you want to visit Yellowstone to see wolves read this book first.
Hawk’s Rest: A Season in the Remote Heart of Yellowstone. Gary Ferguson. The author spends a good deal of time in the most remote part of the lower 48 states. His journal is an immersion into the Yellowstone backcountry.
Large Carnivore Conservation: Integrating Science and Policy in the North American West. Susan Clark and Murray Rutherford. This is a book of six case studies of conservation. A good place to start to begin to understand the problem of living with large predators in a variety of global settings – including Yellowstone.
Roadside Geology of Yellowstone Country. William Fritz and Robert Thomas. This is one volume of the popular “roadside” series. For the drive by geologist it is simply the best source you can find.
Playing God in Yellowstone: The Destruction of America’s First National Park. Alston Chase. When this book came out it it created a furor among park advocates and ecologists. Viewed two decades later it is still controversial but well worth reading for the history and interpretation of events.
Taking Account of the Ecosystem on the Public Domain: Law and Ecology in the Greater Yellowstone Region. Robert Keiter. Strictly speaking this is not a book but a very long journal article from the University of Colorado Law Review. It is still the best source for understanding the legal setting for policy in the parks.
Bear Attacks: Their Causes and Avoidance. Stephen Herrero. This is the definitive book on the data behind the attacks and how to avoid them based on several hundred cases.
Further Readings by Chapter:
Ecological Causes and Consequences of Demographic Change in the New West
The Elders
Yellowstone after the 1988 fires  The articles by Barbee and Varley give some good insights into these two men.
Island in the Rockies
Science, expertise and the public: the politics of ecosystem management in the Greater Yellowstone ecosystem
A Multicriteria Assessment of the Irreplaceability and Vulnerability of Sites in the Greater Yellowstone Ecosystem
What is Conservation Biology?
Wicked Problems
Barriers to Effective Natural Resource Planning in a "Messy" World
Public opinion for sale: The role of policy marketers in Greater Yellowstone policy conflict
Reintroduction and Recovery
Wolf Recovery and Management as Value-based Political Conflict
Creating Conditions for Policy Change in National Parks: Contrasting Cases in Yellowstone and Yosemite
The NPS and Ossification: Does It Still Exist?
Moving Forward
Yellowstone grizzly delisting rhetoric: An analysis of the online debate
Conservation Challenges of Predator Recovery