Q: What causes LOD to turn black at certain angles?
A: The primary cause is using Bloom lighting. If you're using bloom lighting, try switching to HDR or "normal" and see if the problem goes away.
If that doesn't solve it, then there are LOD meshes in your collection that still have vertex color properties attached to some or all of their nodes. This appears to cause all other visible LOD meshes, including the defective one, to emit the color of the node that the vertex property is assigned to. In the vast majority of cases this is going to be black since it's the default emmisive color.
Q: What causes red/yellow/green blobs?
A: The primary cause of these appears to be one of three things:
1. Collision data left behind on the mesh. Including BSX flags and string data settings.
2. Alpha transparency settings on the mesh.
3. The fLightLOD2 setting in the oblivion.ini is too high.
Check the ini file first. Make sure fLightLOD2 and fLightLOD are both no higher than 4000. Anything much past that and the game can produce these anomalies even with vanilla LOD. Users of Cities Alive at Night should check this straight away as that mod's readme tells users to set this value to 15,000 which is off the chart too high.
The actual color of the blob doesn't seem to be repeatable. But it seems to be the catch-all for any number of anomalies caused by leaving behind flags on LOD meshes that don't belong there. BSX flags and collision data seem to be the most common causes.
Q: What causes LOD to turn bright yellow like the illuminated windows?
A: The primary cause of this are LOD meshes with specular data still attached. If that is not removed, you'll certainly be able to cause this to happen. It's pretty obvious, and is so far the only anomaly I've found that also works at night.
One other cause is an LOD mesh with emmisive color settings on nodes that don't need it. Usually caused by changing this property on a window in a mesh and not realizing that other nodes are sharing the same material property settings. The color is not restricted to yellow either, but it usually only picks up on whatever emmisive color is set on the closest "APPLY_HILIGHT" node which is usually an illuminated window.
Q: What causes LOD to get brighter than usual but not turn yellow or some other color?
A: I don't know the cause of this yet and have only see it once in my own game. It happened once at high noon in clear blue sky weather. So it may be related to the sun and HDR lighting. Without more instances of it happening and some repeatable way to make it work, it may never get solved.
Q: What causes black or colored water relfections of objects?
A: This is an unknown right now as well, but there is a chance it's related to the same things that cause colored blobs over LOD objects. So solving those first may solve these. If not, it may be uncorrectable. Fortunately it's not as noticeable when it happens.