Ceiling (105-127): According to the Histogram, the ceiling generally starts around level 96 and is generally all solid by level 105. (The screenshot below, then, is probably a less common case, with the ceiling solid at level 107.) Bedrock appears in levels 123-127. The ceiling is generally all solid, but sometimes caves appear (as shown below). The caves contain random fires and pockets of nether quartz ore.
The ceiling is a GREAT place to build a subway system safe from ghasts, lava lakes, and other hazards. I chose levels 119 & 120, with stations spanning 118-122. This is high enough to avoid any danger of a drop-off to the main nether cavern, though has a disadvantage of having no quartz (which is only at level 117 and below). However, it will still intersect caves which can connect to quartz ore. According to the Histogram, the cave ceilings are all solid by level 121, though all the ones I've found have been solid by 120 (I find them at level 119). Also note that you WILL occasionally hit a random lava block, even in the 119-120 range, so be prepared! (Some people suggest building a trench next to your main subway tunnel for the fast lava to flow into, instead of YOU.) Based on this new analysis, I'd say it's pretty safe to drop the subway tunnel down several levels and still avoid drop-offs to the main cavern (unless you want to avoid the caves).
To get DOWN from the ceiling in survival mode, carefully dig stairs until the bottom opens up. Then drop sand or gravel one by one until the stack reaches you. (You may need a LOT of sand.) Then you can hop on your column and dig down one by one. You can build a traditional staircase or ladder to get back up.
Glowstone is supposed to be available in the ceiling (up to level 120), but I haven't found any yet.
Upper Cavern (66-104): Between the ceiling and lake is a huge cavernous area spanning about 73 meters. Sometimes this span is completely open. It immediately becomes obvious that this is not a friendly place for humans - e.g., where in the overworld can you find a drop of 73 meters? You will need to build staircases and ladders to bring some sort of order to this treacherous land.
Cavern divisions are somewhat arbitrary as walkable "platforms" can appear at virtually any level. However, according to the Histogram, gravel can only occur in levels 60-65. Also, it appears that soul sand can't appear above level 65 either except in fortresses (not confirmed but seems likely). Accordingly, this "gravel belt" makes a nice division roughly halfway up the cavern. In the second screenshot below, you will see a "soul sand belt" around level 65. So everything above that we can consider the "upper cavern" and everything below the "lower cavern."
In the screenshots, the upper cavern is neatly subdivided into lower and upper parts by a platform around level 88, but, of course, cavern contents can vary widely. Apparently fortresses can penetrate the upper cavern (up to level 94), but I still need to find one of that type to do more analysis. (I'm guessing up/down position of fortresses can vary by 30 meters, based on nether wart positions from the Histogram.)
Lower Cavern (32-65):
The lower cavern looks almost the same as the upper cavern except for the presence of soul sand and proximity to the lava lake. Also, nether fortresses can be found in this area, as shown in the screenshots below.
The large lava lakes are always at level 31. According to the histogram, they are usually 8 meters deep, though in my chosen cross section it's only 7 meters deep. The nether fortress pillar extends to the same depth, as it stops at the first rock (non-lava) block to secure its foundation.
Mantle (levels 0-23):
The bottommost levels are supposed to be very similar to the ceiling, except slightly richer in nether quartz (available in level 7 and higher). Based on explorations done so far, the mantle DOES seem to be fairly safe to visit - i.e., that the large lava lakes will not penetrate the mantle. However, as with all levels, there ARE stray lava blocks. It also may be a challenge to get IN to the mantle; you have to find where the large lava lake is absent OR sink sand or gravel in a 3x3 pillar in the lake (then tunnel down the middle) OR tunnel down the middle of a fortress support pillar. You'll have to leave the same way you went in (or build a portal) as tunneling up to the lake is suicide.
According to the Histogram, there's supposed to be mantle caves. I've only found one so far, and it was a tiny "dud" cave. There are probably more practical places to get nether ore. On the other hand, it would be the ideal place for a secret under-lake base.
UPDATE, JULY 2016: I finally found a mantle cave. There was a vertical entrance to it in a non-lake area, and the cave was a pretty good size. As expected, it was a good place to find nether quartz ore. Verdict: These mantle caves are nifty, but hard to find. Also, be careful, there's probably only one exit.
Click here for a Pinterest pin version of the Nether Cross Section in a single, tall picture.