Sample:
Of course, a floor light that low makes no sense to have it shine so brightly in the ceiling infront of it. It's also weird to have a noticeable shadow like that above the crate on the ceiling. In other words, this is what you have.
Spoiler: Current situation (Open)
Looks alot cleaner and makes more sense.
Spoiler: Desired Effect (Open)
Go back to your map, and identify the weird sectors. Go into 3D mode and raise those sectors up up up, and DO NOT texture them. This is really important, as it creates the effect of a smooth ceiling. The surrounding texture "bleeds" and overlaps the missing textures, creating the illusion.
[spoiler="Image (Warning: Big!)]

And that's all there is to it! For basic smooth ceilings like this at least.
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Exception: The method above works only for smooth ceilings. What about a complicated ceiling with borders? This method is slightly convoluted and involves more work than the other method. I'm pretty sure that there are other ways, but this is how I do it.
What if something like this happens? You can't bring your ceiling up since your metal bordering would show through and thus ruin the bleeding effect.
Spoiler: Exception (Open)The trick is to create the bleeding still. Go back to editor mode and create a 1px border around the metal like so:
Spoiler: 1px border (Open)Then, go back to 3D mode and raise everything but the 1px border.

In game:
[spoiler]

Oh no! The light bleeds! Don't worry, go back to sector editing and return the brightness of the 1px sector to normal. It might be weird, but it achieves the desired effect without any trickery.
Spoiler: Now do this (Open)Here it is again. You might notice the 1px of random darkness, but it's easily covered up by items or corpses. This clean cut example is made for demonstration purposes.
[spoiler]

What about the metal bar? You make another 1px border and raise that too. That tallies the weird darkness to 2px.
Sample wad:
http://www.mediafire.com/?dnlokrbtxzr3kem
I hope this helps a few people. If there are any blatant mistakes, I'll edit and redo parts of this.