I wanted to see how good Time Machine was at keeping a complete backup, so I ran a diff between my disk and its latest backup. I was quite shocked to find that there were differences in places other than caches, logs, etc. which Time Machine does not back up.
Time Machine has forgotten to backup (i.e. the latest backup still contains the old version) two of my applications that I updated by downloading new versions in a DMG and copying them to /Applications, and also a Widget in my ~/Library folder. I also found a document in my documents folder that was backed up with the same modification date as the original, but with different content. This is very bad.
If you want to check your Time Machine backup, run the following command:
Mac OS X Hints
http://hints.macworld.com/article.php?story=20071109024812437