Open xterm and run top, or install Conky. They can show you what's using CPU time. Hopefully something will be, and you can identify it and proceed with trying to figure out why it's acting up.

The usual suspects are apt-worker and tracker indexer/thumbnailer.

If your tracker has gone crazy you can reset its databases and cause it to do a full rebuild (only takes a minute or two) by opening xterm and running "tracker-processes -r"