I've discovered that going 100% vanilla fixes the problem... I think there's something wrong with how people make texture packs.... as trying several different packs reproduced the problem, but vanilla always works fine. Talking version 1.4.2
Yes, I have noticed a "freeze" when any sound file initiates. Turning off the music helps immensely with that aspect of our problem. I hope this info helps a little, trying to think of everything related to this.
(BTW... I have given java up to 12gb of RAM... makes absolutely no difference)
I have this issue too... however for some unknown reason, my system recovers from the issue before the CPU usage hits 100%... on the other hand, the "lag" spikes come quite often.
I have reproduced this in 1.4.2... villagers and stairs seem to be a great trigger. Have not found anything unusual about the topography when monsters fall through the ceiling tho... but only those that jump (spiders, slimes) glitch through the floor above.