Quote: "what 3d engines are out there that arent dx or opengl"
Direct3D and OpenGL are both graphics device APIs, meaning they provide an interface between a graphics device(GPU) and an application(such as a game). Other than software based renderers that are used for offline rendering(raytracing and such for 3DS Max/Maya/etc), there pretty much aren't any alternatives these days.
As for 3D Engines, these wrap the graphics APIs and provide higher level features, such as object formats, post processing, levels, materials, etc. There are hundreds of these, DBC/DBPro/GDK being just 3 of them.
Quote: "Also, what order does the pipeline (i guess you could call it that) process the 3d data??"
http://msdn.microsoft.com/en-us/library/bb219679(v=VS.85).aspx
http://msdn.microsoft.com/en-us/library/bb205123(v=vs.85).aspx
Quote: "Yet another part to my question--how is a 3d model stored in a file?"
Meshes are usually stored as a list of vertices and indices, along with rules about how to use them, usually every 3 indices creates a triangle.
