Ubuntu Gamer posted a how-to about using Game-specific Wine Prefixes

Sometimes you need to install some extra stuff into a Wine prefix to get an application working. If you are installing many applications and games your prefix can bloat up. Perhaps you may install something to get your second application working that breaks the first one. Perhaps you have an application that requires Wine to simulate Windows 98 and another application that only runs on XP and above.

To avoid this situation you can create a fake Windows installation for each individual application you install. You can tailor this installation for the application you are installing without the risk of breaking any other installed Windows programs.

  HOW-TO: Using Game-specific Wine Prefixes