Errata

-local should be --local

Use of "throw":

You almost surely mean: raise

The Facility class deletes a person from the population when they occupy a facility, but this should have been done when the person entered the queue. As it is, you could have a person in the queue decide that he has to go again and rejoin the queue at the end (somehow retaining his original place at the same time). Check it out -- for big populations the queue size grows larger than the population.

R warns when you run this script that mean(data) is now deprecated.

mean <- mean(data) should now follow the same pattern as median and max:

mean <- apply(data,2,mean)

"unless queue.empty?" should be "until queue.empty?", as it was in simulation 1.

As it is, you're erasing your queue every turn (you're duplicating the queue, deleting the original, taking one off the duplicate queue, and erasing the rest).

In the code sample, there's no reason to require rubygems, and the restroom require needs to be relative to work on ruby 1.9 (ie, require './restroom')

The line of code:
data[population_size] << restrooms.inject(0) {|n,m| n + m.queue.size}
stores the total number of people in all queues. This does not produce the graph indicated in the analysis section.

Rather, the code should store the number of people in the smallest queue, something like this:
data[population_size] << restrooms.min{ |a,b| a.queue.size <=> b.queue.size}.queue.size

The text instructs the reader to "change the filename from simulation1.csv to simulation4-1.csv". The reader should actually change the filename to simulation3-1.csv.

... we used Ruby to extract messages from a Gmail account using SMTP.

Should be IMAP instead of SMTP