The most annoying part of this game is the maze where you have to find 16 brains. Here are their locations in a little more detail:
-5 brains are found in the large main hall, one of them is hidden behind the brain machine
-7 brains are found in the 4 heart rooms, usually one on top of the walkways to the hearts and one below on the bottom floor (one heart room has no brain on the bottom floor)
-4 brains are found at dead ends of the maze, these dead ends are all on lower ground with respect to the majority of the maze

The level has a perfect mirror symmetry.

Stay on the upper part of the maze until you find one of the heart rooms. You can locate them by the sound of a beating heart, turn your music volume down to hear it better. 3 of the 4 heart rooms are connected: You can easily find them by hugging the wall inside one of them and following it without dropping down from bridges. If you get to the main room, simply turn back and follow the wall in the other direction to find the missing ones.

Next, drop down to the lower part of the maze (you can drop down from those bridges or take the stairs down). The lower part of the maze consists of two separate, very long tunnels (at the ends of which lie the last 4 brains). First, stay down there and find the 2 brains in the current tunnel.

There are a number of steep stairs leading up from these lower grounds. Don't take them, instead follow the path branching away from the tunnel that seems to be level floor (it is located opposite one of the stairs). After some time you will see that this is not level at all, but that there are gradual steps up in longer intervals.

After following this way all the way up you will find the last heart room. Going past the heart room down on the other side leads to the second tunnel where you will find the last 2 brains.

After that you can take one of the steep stairways up and you should be able to see the main room again.

Edit: Someone called Derell Licht made a map by hand (also attached to this post for download):
http://www.flickr.com/photos/derelllicht/4737262122/

Thanks for the information, I am sure it will help a lot of people. Every time I play this game I manage to blindly stumble my way through the brain maze, but it's nice to have some... detailed instructions. I just re-played the game, in fact (thanks to GOG!), and it took me about an hour of aimless wandering before I found all of the brains. A vast improvement over the... what was it... 5+ hours it took me to locate them on my previous play-through (which happened to be years ago, mind you).

Thanks, this helped me to FINALLY get past this part. I like this game, but I'd like it a lot more if the developers weren't so enamored with obnoxious mazes.

Thanks for the tips and map link, Lafazar! That will come in handy.

I didn't think that the designers could come up with a sillier maze than Raquia. Boy, was I wrong. ;)

You're simply great! I was going mad ;)

Not that the brain maze isn't a little annoying, but by far the most annoying part of this game for me, every single time I've played it, has always been this thing (see attachment). I have yet to deal with it by anything other than painful, frustrating, confusing trial and error. I hate it so much. By comparison, everything else is great :)

Can't thank you enough, you saved hours of my life:). I really like the game this far, but puzzles in "hell" are really silly, for me they are the low points of the game. Other than these frustrating puzzles, this is definately a 5 star game:).

Thank you SO much for the map! it took me hours to look for one brain and kept going around!

Related:
In Chapter Seventeen Father Of Lies - this is a map of the entrance of the maze:
http://i.imgur.com/DSvblMK.jpg
This is a map of how you get out of the (shifted) maze:
http://i.imgur.com/xI6z50X.jpg
I just made these using old school techniques, and hereby offer them in the BSD license :)

Keep in mind, if you follow the instructions and can't find all the brains, they don't always all spawn. It's a known bug and has happened to me at least twice.