I must say I disagree with the default ubuntu/compiz setting that keeps indirectly rendering fullscreen windows. This is the correct setting, but only in an ideal world where the driver stack is perfect and compiz is much improved, but for now as you can see from this article, it causes slowdowns. But in my experience it is worse than shown by all these inane benchmarks. In some situations, such as with the nvidia binary drivers, having compiz enabled you can pretty much be sure that compiz or anything running full screen or within the compiz desktop will not be vsynced, or be vsynced badly, for example, frame cadence issues in movies, and tearing in quake live. These vsync issues with compiz enabled happen even if you have vsync set in the nvidia control panel.
The best solution, for nvidia users as of right now, IMO, is to keep compiz running, because its pretty, but enable the option in compiz control center (under the general tab) of "unredirect fullscreen windows" The only side effect of this setting is a very fast flickering when switching from a fullscreen application (pretty much a game or full screen movie only) back to the desktop, its really not that bad, and what you get from it is great: Your videos will have perfect vsync and the correct frame cadence and there will be no performance drop or other vsync issues with games.