In random time intervals, Minecraft takes 100% load on all cores and completely freezes for a couple of seconds. Freezes come in series, i.e. they happen more common for a few minutes and then become less frequent.
They happen in Vanilla singleplayer, no idea about multi.
Tested sound, checked if it is chunk saving and it seems uncorrelated to those.
I would put my bet on light calculation, it may be happening during sunset/sunrise and on new chunks generation, loading and refreshing. The freezes has been happening for a few versions now (since 1.4.2 I think), so it may be connected to code light fixes.
The issue seems exactly the same as MC-535. But that one was deemed "invalid" for allegedly being reported for modded Minecraft.
Comments

Graphics used for running Minecraft:
Intel® HD Graphics 3000
Linux kernel version is 3.6.6
I will try running Minecraft using nvidia card, too
Edit:
Same using
GeForce GT 555M/PCIe/SSE2
driver: NVIDIA 310.19
by Bumblebee
Also, the freeze can occur during level loading, after server startup before "downloading terrain" shows up.
I also have this issue. Same symptoms (different freezeless time intervals, cpu 100%). After these freezes log message appears:
[WARNING] Can't keep up! Did the system time change, or is the server overloaded?
No mods, single player.
Linux kernel 3.6.11.
AMD FX8120, 8Gb RAM, NVidia GTX650 (310.19 driver).
Latest lwjgl binaries from developer site. Minecraft update 1.4.6->1.4.7
And now I don't have such freezes.
Is this still a concern in the current Minecraft version? If so, please update the affected versions in order to best aid Mojang ensuring bugs are still valid in the latest releases/pre-releases.
No answer on querry, assuming no longer an issue.
What kind of graphics do you have on your system, and is the driver up to date?