I've been monitoring top during the update process and have noticed a few 
things.
frequent CPU users are:
synaptic
xorg
dpkg
apt-check
gconftool-2
There are usually two processes for synaptic, they both seem to spend most of 
their time waiting or idle, but sometimes spike. 
Gconftool-2, when running, uses near 100% cpu, and was the only single process 
I could point to as having used massive amounts of the CPU. 

However, during the most severe spikes, Top actually froze itself for
anywhere from 4 to 20 seconds, leaving me uncertain what was going on
during those periods. The interesting thing is that either all live
updating items were paused/frozen, too, or the CPU did not scale up from
800mhz during this time stretch (in other words it seems like CPU
frequency scaling was possibly not responding to the package manager's
load, a state which could turn 50% load into 100% load).

-- 
updating near freezes system in extremely nonlinear way
https://bugs.launchpad.net/bugs/273829
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