The existing answers have already provided some very interesting examples and I'd like to add a few small things, even if they're not directly referencing particular movies or not too obvious or relevant. Of course there's all the more general Western themes probably discussed in your links already, the whole New Mexico setting and the many scenes shot in the nature, especially the New Mexico desert, the acoustic guitar music, the great train robbery Walt and his gang are performing in S05E05 ("Dead Freight").
But it's interesting that you bring up the point of "subverting the Western genre", because there is actually a scene in S03E12 ("Half Measure") which, while not referencing a particular movie, plays with one of the most traditional Western scenes ever. At the end of the episode Jesse is facing the two dealers who killed Tomás (Andrea's little brother). The way those two parties quietly approach each other, knowing and determined of what's to come, the closeup shots of them pulling away their jackets and readying their guns, the consecutive shots of Jesse's face getting closer and closer, the wide-angle shot of the opposing gun holders. This whole scene as well as its cinematic presentation very much resembles a classic gun duel showdown as known from virtually every Western ever.
But all this elaborate and suspenseful construction does not get resovled in a classic Western way of the one duelist who draws quicker winning. No, Walt, being as to this point a complete outsider to the scene handles the situation in a very untraditional but effective way by just crashing the dealers away with his Aztek. If this is not a subversion of one of Western's most innate images, presented in a cinematographic style that very much acknowledges this reference, I don't know what is. (You could say Walt is an intruder to the whole situation, handling it in his own original way, not by strength or experience, but by quick thinking, ruthless initiative and, let's face it, luck, afterall very reminiscent of his overall venture into methamphetamine business.)
Just while thinking about one of Spaghetti Western's greatest examples I stumbled across another possible reference in nothing else than the great finale of the show. At the end of the very last episode S05E16 ("Felina") Walt gets his final revenge on Jack's gang by visting their supposed trap but suprising them with the remote controlled machine gun he has in the trunk of his car, effectively mowing down nearly all of Jack's men.
This could be seen as a reference to one of the most remarkable scenes in Sergio Corbucci's 1966 classic Speghetti Western Django, where Franco Nero's eponymous protagonist enters a town dragging a coffin. And once he confronts the gang of the man he's seeking revenge to, he opens his coffin and pulls out nothing else than a big-ass machine gun, mowing down most of the gang.
Another reference I found is of a much more far-fetched and rather non-Western nature. But there is the bottle episode S03E10 ("Fly") where Walt is trapped in the lab with a fly and getting increasingly paranoid of its supposed contamination, slowly losing his sanity over it. Call me a lunatic, but this actually reminded me of the famous opening scene of Once Upon a Time in the West, where one of the hitmen waiting for Harmonica is repeatedly bugged by a fly and ultimately traps it in the barrel of his gun.
Like the Breaking Bad episode, this scene, albeit being utterly irrelevant for the actual further plot of the movie, has been the source of much discussion and analysis. Decide for yourself, though, if this is a bit too far fetched of a similarity to actually call it a reference to Western cinema.