i can confirm that this problem occurs in lucid version of distributions 
Kubuntu and Xubuntu.
it really sucks.

to make it better:
the relevant line 8 of /etc/cron.weekly/apt-xapian-index is (where $CMD is 
update-apt-xapian-index ):

        nice ionice -c3 $CMD --quiet

we can have much more than this:
- give a nice level of 19 instead of default 10
- enter a missing space so ionice will do its job
- make the indexer update only NEW packages instead of the whole database (as 
suggested by MarcS in comment 31)

this will get the most silence without dropping the indexer altogether:
- tested that the indexer will silently exit if database is already built
- tested that a 800mhz/256mb xcfe box stays responsive while indexing with the 
new nice/ionice pattern
which fixes this issue for me.


** Patch added: "xapian responsiveness patch"
   http://launchpadlibrarian.net/47372943/xapian-363695.patch

-- 
update-apt-xapian-index uses too much CPU
https://bugs.launchpad.net/bugs/363695
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