After some days of my machine working it also happened to me.
(sorted top)

top - 09:34:28 up 10 days,
[...]
2614 root      20   0  334m  43m 7756 S 14.9  5.0 269:54.61 Xorg
[...]
3171 chochis   20   0 46728  27m 3088 S  0.3  3.1 366:35.31 indicator-apple

How this can use much more cpu that Xorg?
I have noticed before too:
I have pidgin working all day but sometimes my internet connection crashes, so, 
it has problemas reconnecting, when this happens, notification applet goes with 
the envelope and a green dot and after that it starts to be cpu greedy and 
never returns to normal behavior.

Regards

-- 
High CPU usage 
https://bugs.launchpad.net/bugs/368631
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