Where might I find some thoughtful philosophical or critical readings of The Matrix, in particular which treat the primary theme of virtual reality?
There is a book published on precisely this topic.
The question, as asked, is a pretty useless one. If you have taken a basic philosophy course and seen the film, it's pretty trivial to recall the film and make a list. If you haven't taken a philosophy course or seen the film, any answer will be useless.
Since there is a book on the topic, that would be the best available option for someone who does not wish to do the actual thinking themselves.
The question, as written, reduces to "Do my homework for me." Since philosophy insists upon the necessity of doing one's own homework, I personally make sure that any answers I give here are of the sort that will provoke more thinking, and not help someone avoid thinking.
Now that the question has been edited to mention virtual reality, I'll add a couple bits.
The obvious reference in this regard, of course, is Baudrillard (whose book on Simulacra appears as an object in the film), but on a more fundamental level, the deeper reference is to Plato's Republic and the allegory of the cave.
That being said, the Matrix reads largely as if a first-year philosophy student attempted to make a science fiction film, so the references are clear and plentiful.
More generally, the theme of virtual reality is covered fairly deeply by Baudrillard and to some extent Paul Virilio (note that a hollowed-out copy of Baudrillard's Simulacra and Simulation appears in one of the earliest scenes of the film.)
For a somewhat different take on the problem of simulation in general you may wish to compare de Landa's Philosophy and Simulation.
Finally, there is this popular collection of essays on the film (including one by Zizek) which may be worth looking at if you haven't already.
May I add the Video on the philosophy of the matrix
NOTE: Yes I know it's not a book but I think it will help those who want a fast introduction into the philosophy theme of the matrix
You might want to ask this on scifi.stackexchange.com instead? Here's a reference from 1960 to wiring humans to technical equipment making a loose brain think it has an entire human body: http://en.wikipedia.org/wiki/William_and_Mary_%28short_story%29 If you want to define virtual reality verbatim you may want to look at VRML which is a VR modelling computer language for virtual worlds and if you are interested in a physical analogy there is the concept of virtual matter i.e. virtual photons and photons you can ask about on physics.stackexchange.com and in business there is the company Linden Labs who make the virtual worlds secondlife.com which is mora like a game you can explore while the philosophical tone and background can be interpreted as a matter of difference between existence (like nature exists independent of the mind) and existence in the mind (like a concept only exists in the mind.)
So there are choices you can make if you want to explore the physical, philosophical, sciencefiction or simulation meaning of "virtual reality."
There is also the science fiction novel called Better Than Life by authors Grant / Naylor about people entering a virtual reality game and can't know that it's a simulation / an induced dream. You could also research the concept of hyperreality and how hyperreality is distinct from virtual realities is what most philosophers agree on: Whether there is just one "reality" or many "realities" where a physicist and logician probably says that there can be only one reality while philosophers may understand that there could be many different realities - both views are current.
Seeing as how I seem to be in the habit of throwing my comments in months after questions are answered... ;-)
Personally I can't give you any critical readings or references to peruse... Unlike most others on here, I'm what you'd call more of a "stand-up philosopher". Seriously though, I think that you've misunderstood the film if you believe that the primary theme is virtual reality. The "matrix" itself is merely a vehicle to tell a particular story, and to provide a context within which the machines can interact with humans on a level that the audience can relate to. This was a film made more for the masses rather than the hard-core sf geek community, so having a computer spit out l33t text on a suspiciously unix-like screen just wouldn't cut the proverbial mustard. Therefore, the matrix provides context for the story, much like the starship Enterprise does in the Star Trek genre.
The themes are themselves quite obvious once you let yourself look beyond the really cool effects and the Kung-Fu. The primary ones being the struggle for freedom from slavery and for self-determination, self-sacrifice and selfless service for a greater cause.
Much of the first film has overtones of a struggle between good and evil which becomes more obviously defined by the last film, although since your question was about The Matrix then I suppose that my answer here should note that in the first film the positions of good and evil are very subjective and not entirely clear, even if you did find yourself sympathizing with the humans in the film and thus feeling that on the surface it was the humans representing the good and the machines the evil. That said, even by the last film, each character has acted entirely within it's own nature, so the good and evil themes are still quite "muddied" IMHO.
The "thematic distraction" of the classic good vs evil sub-plot seems to stem from another very strong theme which many might at first glance assume is about religion, but which I think is more about belief and faith. I find that this is perhaps the stronger and more poignant theme in how it is played out. Firstly as depicted by Morpheus' unwavering faith in the Oracle's prophesies and his belief that Neo will turn out to be "The One", and secondly in the abilities of all of the bad-ass humans constantly wearing dark sunglasses who need only believe that they can do something in order to bend the rules of the Matrix to do some of the really cool jaw-dropping stuff. The first is a theme about having faith in others, and the second is all about believing in one's own self.
Of course, we can try to draw a lot of really interesting philosophical stuff about the films, but personally I prefer to simply enjoy them as a really cool series of Sci-Fi Kung-Fu flicks with an awesome soundtrack! :-)