Thanks for the detailed critique, Enjay.
Most of what you've said I agree with or was a mistake of some sort. If you think it's a bug, it probably is, like the zillion apple thing. I'm not sure what you mean when you say "first, second, third, etc..." room. If you could use their names, that would help a lot. For example, Room 1 = Hero's Demise, Room 2 = Decaying Hall, etc... Was the text working, indicating where you are and where a door leads?
Glowing Ticks - I made no new assets. The glowing ticks are a more durable golden version which drop lots of money. Unless you're seeing glowing effects on the normal ticks and I'm misunderstanding you?
OK, now it's time for the harder stuff. The darkness is something I'm fond of, but I may definitely be in the minority. If I make it light enough to see through it, why have the darkness be low at all? But at the same time I don't want it to be a problem. I think you hit the nail on the head when you said to save it for particular areas. The idea is to encourage you to stick together, like back-to-back, when venturing in the darkness. I mean this is basically an abandoned prison with a dark magic around... anyway, not totally sure how I can use it without it being weak. If I'm going to use darkness, it has to be
dark. I also tried to have a theme of, the deeper you are in the dungeon the darker it is. So, in the West Wing (the bit you played), you've got the Decaying Hall with some light to see, but all the offshoots are pitch black, because that's the lowest. Going 1 layer above the Decaying Hall and you have plenty of light. Thoughts?
I tried to make some connection with the name of the area and what you found in it. It wasn't always smooth. The Chambers of Treachery were supposed to be torture chambers. There's only 4 large cells, a blood pit in each one and a larger blood pit in the center (couldn't find any other doodads to help support the theme). I put the random traps there as a throw back to... there's sharp stuff around here. :| ha ha, it's weak, but it's the best way I could think to have traps planted in a jail!

In the first room, the secret room you can either enter through the glowing eyes, or break into from a cell is empty. Finding secrets is fun, finding empty secrets just makes you question what you're doing with your life.
This seems to be an issue. What actually happens is you break down the wall and exit through the glowing eyes. This is how you break out of your cell at the very beginning. You can later enter that cell. I may just remove the glowing eyes or not allow the cell to be opened.
Your map doesn't use the color cover doodads in the editor. You probably want to find these and use them, as it will make your interior spaces feel like they're inside (Creating a sharp contrast between walls that you can be on either side of, and walls where you're on the only side of).
These are a pain and don't work with black being my back color. If we could have black colored pieces like they gray ones, where I can hide things under them, that would be great. But you're right about readability on knowing if you can get to the other side or not. We'll see.
Always have a reason for everything. Those buttons at the beginning that open the doors right next to them? They're decent, in the sense that they allow you to bypass all the enemies in the cells if you want to, but then what reason is there for pushing them? An apple? Well, you're not fighting anything, so there's no need for that. Maybe try ditching the individual buttons, and at the furthest corner of the level, have one button to open all of the cells, letting loose the hordes of baddies, and allowing you to go in and collect that sweet sweet gold, and those precious bronze keys.
Give the player reasons to want to do things. As it was, I made it up to the fourth level (The one with tons of slimes and the elite skeletons thrown in) before I stopped, and I only made it there because I had a reason for playing (Helping out the custom level community, by giving the advice you're reading here). If it weren't for that, I probably would have made it half way through the first set of cell-blocks, in to the second set, saw it was the same, and then quit. Give reasons to continue. Oh, you want that 5-up? You want those stacks of fat cash, to purchase the upgrades from the vendors, hidden behind the silver doors? Well, now you've gotta find those keys, and that cash, you have to find the secret passages, to solve the puzzles, to get the rewards.
I haven't properly placed rewards, various collectibles, and I'm randomizing positions of a lot of goodies and keys. That may explain a few things. In short, I'm not done, but wanted feedback to help. Additionally, I don't agree about
always. You're in a jail and you don't know where things are. It's OK to stumble across a malfunctioning cell door button, a relatively empty corridor, or whatever. Ever played Diablo 2?
I do agree it's not OK to have an entire area/room and have no reward, and highlighting key things like a button that unlocks a secret or opens a new way with a chime or a graphic is a good thing, but the small stuff? I think it's OK to get a little crazy with it. It's fun to push buttons.

By the way, is it normal in HammerWatch that silver keys are only goodies? That what I was planning to do: bronze and gold keys for progression where silver keys are optional for goodies.