Where did the command-backtick keyboard shortcut go in 10.7 Lion?
This feature is still present (I'm using 10.7.3 and it works for me).

Go to System Preferences > Keyboard and check the keyboard shortcuts. In the list of 'Keyboard &amp; Text Input' shortcuts you should see 'Move focus to next window'
⌘+`. 

Make sure it is checked, and it should work.