It appears that a previous feature, namely the ability for Terminal's window focus to change with mouse movement, is broken in 10.6 and causes Command-Tab to not transfer window focus correctly. To fix the problem, just paste the following command in a Terminal:
defaults write com.apple.Terminal FocusFollowsMouse -string NO
Then restart Terminal.
Mac OS X Hints
http://hints.macworld.com/article.php?story=20090914134806703