Principles of Animation
[Lasseter87] Principles of Traditional Animation Applied to 3D Computer Animation. John Lasseter. SIGGRAPH 87.
History and Systems
[Catmull72] A System for Computer Generated Movies. Ed Catmull. Proceedings of the 1972 ACM Annual Conference.
[BW76] Interactive Skeleton Techniques for Enhancing Motion Dynamics in Key Frame Animation. N. Burtnyk and Marceli Wein. CACM, October 1976.
Film and Cinematography
[HB96] Movies in the Minds Eye. Hochberg and Brooks. from Post-Theory, edited by Boardwell and Carroll.
[Shoemake85] Animating Rotations With Quaternion Curves Ken Shoemake SIGGRAPH '85
Note: there are many other (possibly better) references for quaternions like Ken's notes on quaternions. Two other things that are worth mentioning are a 1998 article in Game Developer magazine (online) and the appendix to Matt Antone's thesis.
[Grassia98] Practical Parameterization of Rotations Using the Exponential Map F. Febastian Grassia Journal of Graphics Tools, 1998
[Alexa02]Marc Alexa , Linear Combination of Transformations SIGGRAPH02
[Zhao94]Inverse Kinematics Positioning Using Nonlinear Programming for Highly Articulated Figures - Zhao and Badler ACM TOG 94
[TGB00] D. Tolani, A. Goswami, and N. Badler: "Real-time inverse kinematics techniques for anthropomorphic limbs." Graphical Models 62 (5), Sept. 2000, pp. 353-388.
[Bregler02]Turning to the Masters: Motion Capturing Cartoons Christoph Bregler, Lorie Loeb, Erika Chuang, Hrishikesh Deshpande (Stanford University)SIGGRAPH02
[Liu02]Synthesis of Complex Dynamic Character Motion From Simple Animations C. Karen Liu, Zoran Popovic (University of Washington)SIGGRAPH02
Human Figure Animation
[Gleicher99] Animation from Observation: Motion Capture and Motion Editing. Michael Gleicher. Computer Graphics, 1999.
[Perlin94] Real-time Responsive Animation with Personality. Ken Perlin. IEEE Transactions on Visualization and Computer Graphics 1994.
[MFGD99] Computer Animation of Human Walking: a Survey. Multon, Fance, Cani-Gascuel, and Debunne. Journal of Visualization and Computer Animation, 1999
[Hodgins95] Animating Human Athletics. Jessica Hodgins, Wayne Wooten, David Brogan, and James O'Brien. SIGGRAPH '95
[Blumberg02]Integrated Learning for Interactive Synthetic Characters Bruce Blumberg, Marc Downie, Yuri Ivanov, Matt Berlin, Michael Patrick Johnson, William Tomlinson (Massachusetts Institute of Technology, The Media Laboratory)SIGGRAPH02
Motion Capture and Motion Editing
[Shin01] Computer Puppetry, and Importance-Based Approach. Shin, Lee, Gleicher, and Shin. ACM TOG, April 2002.
[BW95] Motion Signal Processing. Armin Bruderlin and Lance Williams. SIGGRAPH '95
[WP95] Motion Warping. Andy Witkin and Zoran Popovic. SIGGRAPH '95.
[Gleicher98] Retargetting Motion to New Characters. Michael Gleicher. SIGGRAPH '98.
[LS99] A Hierarchical Approach to Interactive Motion Editing for Human-like Figures. Jehee Lee and Sung-Yong Shin. SIGGRAPH '99.
Character Skinning and deformations
[Singh98] Wires: a geometric deformation technique.
[Lewis00] Pose Space Deformation: A Unified Approach to Shape Interpolation and Skeleton-Driven Deformation. John Lewis, Matt Cordner, Nickson Fong. SIGGRAPH '00.
[Allen02]Articulated Body Deformation From Range Scan Data
The best introduction to this stuff is Andy Witkin and David Baraff's course notes. I have included the basic pieces here.
An Introduction to Physically-Based Modeling.
[WB-1] Chapter B: Differential Equation Basics
[WB-2] Chapter C: Particle System Dynamics
[WB-3] Chapter F: Constrained Dynamics
Andrew Witkin and David Baraff. SIGGRAPH Course Notes (1995-2000).
Beyond that, there is a lot of different things. I will probably choose some subset of them as the course progresses, depending on what people are interested in. Three that will definitely be required are:
[Reeves83] Particle Systems: A Technique for Modeling a Class of Fuzzy Objects. William Reeves. ACM ToG, 1983.
This is a really seminal paper.
[BW98] Large Steps in Cloth Simulation. David Baraff and Andy Witkin. SIGGRAPH '98
This paper is nice since it really tells you what you need to do to do this. It is the basis of a bunch of commercial software.