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.