(Note: I may eventually add pictures to this. Scans are a wonderful thing, but not if you can't find the large versions of the pages you actually want to scan. I reallly need to organize my Shonen Jump issues.)
I talked about Bakura's soul room in the most recent comic commentary. Obviously, I didn't know how Takahashi would have built it; but thanks to the soul rooms seen in the manga and anime, I did have an idea of how he might have started.
The three soul rooms we see in any detail are those of Atem (obviously) Téa, and Professor Yoshimori, a one-story character who suffered quite a bit of abuse (but didn't die, which is what would have happened to him otherwise.) We see a very little bit of Yugi's: it was bright, and there were toys scattered across the floor. Shadi judges him to have a pure soul with a mere glance, indicating, perhaps, that brightness can mean this.
Each soul room's starting point was something that was important to the character, usually involving interests. Téa's was a dance studio. Yoshimori's was full of books, like a library. Atem was wrapped up in his own mystery and in his death, and therefore his room resembled a cross between a royal tomb and an Escher maze. As noted, we can't see exactly what kind of room Yugi's room begins as-- but the walls have a very modern material look to them, and I'm inclined to believe that it's based off the game shop, a video arcade, or something similar.
If I were to build a soul room for myself, I would start off with an art studio, with off-color furniture and books piled haphazardly around the room in little towers. I have an image in my head of something like Merlin's Tower in Disney's "Arthur."
The decorations and furnishings in the room indicate several things: stuff like trees, shelving, books, chairs, anything that doesn't represent something specific but rather something general, represents aspects to a personality. In Téa's room, the walls were covered with mirrors, which Shadi declared showed her to be either confident or prideful, and that in any case, she has strong beliefs. I interpreted the open ceiling to mean an open personality, and likely the fruit trees indicate generosity of spirit or an outgoing will. Different kinds of trees probably mean different things; in Ryou's soul room, I chose to use willow trees in part of the room to indicate his occasionally meloncholy nature. The books in Yoshimori's room showed that he is a man of learning. He also had a lot of ancient artifacts sitting around in his room, showing his love of the past.
Photographs, portraits, statues of people and other specific things should be taken to represent specific things that are important to a person. Téa had a faceless portrait of a man with a superhero shield on his chest, to represent Atem (who she didn't know at the time was Yugi), and it was sitting on a loveseat. She also had a picture of the Statue of Liberty holding a ballet slipper, which pretty obviously represented her New York dreams. Professor Yoshimori had a little portrait of his family sitting in the corner, covered with cobwebs to show how he had neglected them and now regrets it.
For whatever reason, I like the idea of dead people having curtains and shrouds around their portraits in other people's soul rooms, the way Cecilia's portrait was hidden by a curtain in Pegasus's private sanctuary. This wouldn't always be the case, and sometimes a shroud could instead indicate estrangement or a long separation. In Yukai's soul room (which you WILL eventually see!) there will be a double portrait of his father and Atem, overlapping one another to show how they've sort of blurred in his mind-- but Atem will be turned mostly away, a figure important in Yukai's life, yet a person that Yukai has never met.
How different things are represented can be shown in different ways, especially depending on the person a soul room belongs to. I tend to think that things like trees, water, mirrors and clouds would tend to be very general and usually mean the same sorts of thing from person to person. A dance studio, the style a loveseat is done in, the types and titles of books, would be more specific to a certain person. Whether the portraits are framed images or statues probably won't make much difference, but a gold statue versus a clay one might mean something, and so would the fanciness of the frame. (A statue versus a framed portrait might show how "real" some dream or person is to the soul room's occupant, but your mileage will vary.) The kinds of flowers that appear in a room might mean something specific depending on their prominence and location, but if they're scattered randomly about, they might just be there to add a sense of lushness to the room, or to indicate a full, romantic, or whimsical spirit. The toys on Yugi's floor were probably intended to indicate his playful nature, or his general innocence and sweetness.
Téa's soul room also featured a big smiley sun that reminded me very strongly of the Sun and Moon clocks and art that one of my aunts absolutely filled her home with. I am going to be upfront and say that I really have no idea what the hell that's supposed to represent, because I always found them a touch folky and creepy, and I don't think of Téa as folky or creepy. Maybe Takahashi just wanted to show how cheerful she is. :P (Suns should not have faces, dammit!!) Also, that Statue of Liberty portrait was kind of pushy, because it bounced around all over the room and managed to appear in every single panel. I doubt that means anything, and yet I find it hilarious.
Sources that would be helpful for devising symbology in a soul room would include dream dictionaries, books on religious symbology (Not for imitating slavishly, but for ideas- especially if a character's religion is important to them), and imaginary therapy scenarios. I went on a mindwalk as part of a group therapy session in high school once.* Among other things, there was a path, a forest, a cup along the path, a pool of water, and a wall that stood in the way of the path and went as far as the eye can see in either direction. The way you imagined each of these things and what you did with them was supposed to indicate aspects of your personality and how you approached life. Keep that idea in mind when building soul rooms, and you may begin to find the excercise is actually very fun, and even better, can put you into very deep touch with a character, even an original one.
*(For the curious, my mindwalk indicated that I was quiet and contemplative, but materialistic, that I considered my sexuality mildly forbidding and mysterious but liked to, ah, tease the fish, and that death made me more curious than anything. At the time, this actually described me pretty well. Unfortunately I suspect going on the same mindwalk today would be colored by knowing what each thing represented. You can bet we laughed pretty hard when I said I teased the fish and then found out the pool represented sexuality.)