In the case of MS-Office you have to edit approx. 10,000 registry keys. Sure the software will launch but it's a pain. Fortunately, I found a search and replace tool for the registry and was able to fix all the broken keys. On a side note, there is software that will do this for you. Thought it came with Partition Magic...

Either way, in Linux you would have to change some things hear and there as well. Not nearly as bad as Windows however. No registry keeping paths, etc.