At present, there's three major pieces of functionality missing from the engine:

• A scene graph to organize the objects in the game world; we have a couple of books we can turn to for that (Eberly's books, Game Coding Complete), and I'm thinking of using an octree (http://www.altdevblogaday.com/2011/08/01/loose-octrees-for-frustum-culling-part-1/, http://www.flipcode.com/archives/Octrees_For_Visibility.shtml) to cut out unnecessary render calls.
• A scripting system, so fairly normal people that aren't insane can use this engine to actually do things. The plan is to use Lua along with the LuaPlus helper library to integrate scripting, and create some system of class/subclassing functionality if people need object-oriented programming structures. Again, we have a book for that (Game Coding Complete talks about this a lot).
• An audio system. This is less clear; there's cross-platform solutions, but they cost big people money. There's free solutions, but they're often platform-dependent or just really weird. I'm thinking of making this another module like the rendering system, and just let the OS module decide what to load. I'm definitely open to suggestions on this; under Windows, I'm planning on just using DirectSound (MSDN articles here) because nobody's really explained XAudio2 to me.