Ubuntu – top command on ubuntu multicore cpu shows cpu usage >100%

By default, System Monitor will only display your own processes. You can show system processes by selecting Show -> All processes from the menu bar. Unity itself would never show up in the process list since it's just a plugin for Compiz. So if Unity was the problem, then Compiz would show a high CPU usage. Compiz 0.9 is slower than 0.8, this is confirmed. However, I see no reason why Unity itself should be very demanding, or why you would think so.

11.04 and 11.10 were two very special versions in that there were large amounts of changes in the underlying system. As an example, my laptop had a battery life of about 5.5 hours on 10.04, 4.5 hours on 11.04 and 4 hours on 11.10. I've upgraded it to the development version of 12.04 (Precise Pangolin) and now it's back at about 5.5 hours.

All this is to say that you're not imagining it. Specially 11.10 has been very power hungry, and there is no single piece of software to blame. The Linux kernel has had some power issues as well, for instance. My desktop sounded like a Harley Davidson in 11.10, but not it's completely silent again. So it's a problem with 11.10 in general, and 12.04 fixes it on all my computers. While I don't want to recommend that you upgrade to it yet, at least it should be comforting to know that it'll most likely fix all those issues, and that it'll be available in the not so distant future.

You can check its process ID, with ls -l /proc/1639
and trace its activity with sudo strace -p 1639

According to this thread it's a malware with root permissions.