The regular process for me is:
-Dump room's geometry (Perfect dark is 1 room at a time, while games that are less memory intensive on n64 let me do more at once)
-Dump Textures from said room (both done on 1964 with a special plugin)
-Import room into blender (x3d/wrl supports VRML97 still, which is what n64 used)
-Save blender file if it's the first room
-After the first room is imported, have to move to the next room in the emulator, and repeat the first 3 steps
-Have to grab each piece by a vertex that is common with another room, and snap it into place with blender. This is important to not do it by hand/eye because nothing will line up.
-Once finished, have to merge all meshes into one single mesh, flip all normals, and remove all doubles, then it's ready to go
-Export as .OBJ (blenders quake map exporter sucks, and can't handle odd angles)
-Use a custom build of half life 2's OBJ2MAP
-Done, import into radiant and re-texture.