Books

http://www.bytewave.net/future/design/paradessa/paradessa_library.html - The series, Game Programming Gems, are way cool, there's an article there about Sphere Trees (in Game Programming Gems 2) which is a really good hierarchical data structure for doing culling tests on highly dynamic objects.

Communication

NeL - "Our platform for the next-generation of Persistent Worlds."
Genesis3D - Another OpenSource 3D engine. This engine doesn't door well for expansive outdoors or large rooms. But, it runs pretty quickly and is geared more for first-person-shooter genre.
- world-editor - added this link because I didn't see it linked off of Genesis3D's site...
LithTech - Lith, the engine of a local company. Engine used in "No One Lives Forever".
- NoLF - official site. Source available.
WildTangent
- Multiplayer Overview
3D engines list - a nice site with a big list of 3D engines out there. Some links are a bit dated and broken, but still worth a dig.
http://ogre.sourceforge.net/ - Object-oriented Graphics Rendering Engine (C++)

OpenGL - official site
Mesa - Mesa is a secondary project that attempts to provide an API very similar to OpenGL.
http://msdn.microsoft.com/directx/default.asp - DirectX is everywhere.
- the DirectX eXperience - a slightly dated site with some directx articles of interest.
CSE457 - you probably shouldn't dig this deeply into low-level graphics, but just in case...
http://developer.nvidia.com "

3dLinks - site with some useful links to 3D related stuff.
SDL Games - this site contains some links to some games. Browse it mainly to help gather some creative ideas.
BitKeeper - Source Management. Handles binaries very well. Traditionally, we recommend VSS, but if you're feeling adventurous....
Previous 481's - you should dig around here for more links and ideas of what is and isn't within the realm of possibility
CSE403 - 481 is the software engineering capstone. Don't forget your software engineering skills!