There are two separate issues. Never ever set WINEPREFIX to an existing windows installation, for instance if you have windows on a dual-boot separate partition. Wine will break that windows installation by "updating" Windows with Wine's DLLs. However, if there are programs that you "installed" in windows that didn't really need to be installed, then you can invoke wine with the path to the application. Some applications come with installers, but don't really install anything outside of what it put into it's installed directory (no DLLs in \Windows\System32, no registry entries, etc...). I've run quite a few programs from my windows partition without copying them. That being said, I've also run into problems with those programs. For instance, I often run into a problem where the program is unable to write files because the partition is NTFS or FAT-32.
