In OS X, Spotlight can be used to locate and open numerous file types, including Applications, which makes it quite useful as a launcher utility. If you set up the menu's display order so that applications are at the top of the list, then instead of accessing your applications through the Dock or through the Finder, with a quick search for part of the name you can have the application launched with a few keystrokes. Though convenient, if you have Parallels desktop installed on your system then you may find application search results showing the available Windows applications instead of your desired Mac applications.
This happens because Parallels puts application Windows application references in a folder called "Applications" that is within the user's home directory, allowing you to access the Windows applications as if they are Mac applications, and have them show in the Dock and otherwise be handled similarly to native OS X applications.
At times this feature of Parallels Desktop can be convenient; however, at other times it can be frustrating especially if you regularly use the spotlight menu as an application launcher for Mac OS X applications. Even though Windows applications in Parallels are shown with a parallels icon in them, if you do not take care to check whether the selected application is a Windows application then you may inadvertently launch your virtual machine and have to wait for it to load and display the application. Furthermore, Spotlight seems to prefer choosing the Windows applications instead of the Mac option, making it even easier to inadvertently launch a Windows program through Spotlight.
The inclusion of this folder in Spotlight's indexing is what causes its contents to show up as available applications, so if you add this folder to Spotlight's privacy list then you can prevent it from being included in the search results. To do this, first go to the Spotlight system preferences and then click on the "Privacy" tab. Then go to your home directory and you should see a folder called "Applications" in there. Within this folder there should be a subfolder for each Windows-based virtual machine you have set up in Parallels Desktop (i.e., "Windows XP Applications," or "Windows 7 applications"). Drag these folders to the Spotlight privacy list, and from now on you should be able to use Spotlight to access only Mac applications.
Even though you have prevented the Windows applications from being launched in Spotlight, you can still make use of them by launching them directly, or by adding the folder to the dock as a stack so you can quickly access them.