Played through this right up to the point where I got to the glitched water. I decided to make some edits to the first room of this so you'll an idea of what looks good in a DN3D map. Don't take it the wrong way; I'm genuinely trying to help, not show you up or anything...

First thing I did was take the windows on each wall and drag them to where they would be positioned in the center. I also added drew a few extra sectors to make some "curtains". Note that I also re positioned the pane (ie, the transparent wall) to where it was in the center of the window's sector, rather than on the outside. Doing stuff like that helps add some depth to the architecture.

Next thing I focused on was the doorway that led into the following corridor. Arwu was a bit off when he said that the ceilings need to all be the same height; they don't. It looks a lot better if you bring doorways like this down by a few units so there's a clear distinction between the room and the hallway. Also, you might notice that I added a few extra sectors around the doorway to create a sort of "frame" for it. This is sometimes referred to as "trimwork" and it always makes a map look more interesting.

After that I decided to tackle the lighting fixtures and shading, or rather, the lack thereof. Pretty much every part of your map is at a shade value of 0 or lower, but there's no lights anywhere. I started by making one big sector that encompassed nearly the entire room, then started making smaller sectors within it. After all that was said and done, it wound up looking like this in 2D mode...

The small sector in the center of it all (where the white arrow is) is the light fixture itself. All the bigger sectors surrounding it are put at different shade values. This creates a nice, gradual change in the intensity of the light, which you can see in the first and second screens. After that, I darkened the walls at the very end so they'd match the floor, then I added that extra "door" in the back. It doesn't actually lead anywhere, but putting stuff like that in helps add immersion to the map.
Mind you, doing all this stuff was pretty easy (it certainly didn't take knowing any special keys or tricks in mapster) and IMO it made this room look way better. It's just my advice, take it or leave it, but this is how I'd go about doing it, and it's probably what a lot of the other guys that have critiqued your maps are looking for.