NOTE: If this video won't play, you should be able to watch it here - Trust My Coon Sense
Additionally, Alex DeLarge shows up in the extended movie-length version of Imaginationland, amongst the villains. Absolutely great film by the way, I highly recommend it.
There are other A Clockwork Orange references in the show, but these two are the most obvious.
Even in the original South Park movie, when Cartman has the V-chip implanted in his brain & we watch him being tested, suggests a loose parody of the similar scene in ACO. Brilliant really.