Does a messier room actually have higher entropy?
A room can be a complicated system, (at least mine can be) so I shall assume a simplified version: an enclosed space bound by 4 walls, a ceiling and a floor and the only piece of furniture inside the room is a desk, and  two books on it -- book 1 and book 2.  

In the this scenario, I would define a clean room as one with both the books neatly stacked on the desk, and in a messy room you can find one of the books on the floor. 

Now, if I were to try enumerate the number of ways of organising the books in a clean and a messy room, I would find that there is exactly one way in which I can achieve a "clean room configuration", and that is by having both books on the desk. On the other hand if you wish to achieve a "messy room configuration", you can do so in two ways-- either have book 1 on the floor and book 2 on the desk, or have book 2 on the floor and book 1 on the desk.

The no. of ways in which you can achieve a configuration is called its weight and is defined as:  

$$W = \frac{N!}{N_0!N_1!N_2!....}$$ 

In the first case, $W=1$ (clean) and in the second $W=2$ (messy)

The boltzmann formula for entropy is: $ S = k_b\ln W$

Plugging in $W$, we get $$S_\text{clean} = 0$$ and $$S_\text{messy} = k_b\ln2$$

Thus, the messier room has a higher entropy. This somewhat "silly" argument can be reproduced for a room with more furniture, and more items in it. Feel free to toss in some clothes, papers, chairs, book cases, toys, shoes, pets...go nuts.

So, I believe the analogy holds good. But again, what I did here is a silly exercise to illustrate a point, and it isn't meaningful as such. 

If you wish to learn more, watch this lecture by Leonard Susskind