Try a clean install, or use pydefrag. Fragmentation <i>does</i> happen on Linux filesystems when they get too full, and the number of updates you're constantly installing for Maverick is probably doing some work on /var/cache/apt/archives. I had my boot slow down considerably from Jaunty to Karmic (or was it Hardy to Jaunty?), and a reinstall helped, since then only what should be there was in / not everything that ever was.
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