I’ve been migrating most of a clients files (but not all) to Windows SharePoint Services 2003 to give them version control and better access. One of the things that I had forgotten about was that SharePoint has a much larger list of characters it doesn’t like in file and directory (folder) names. You can look at the KB905231 for details.
I wrote a quick command line utility which will process an entire directory structure and make whatever replacements you would like in the file and directory names. It’s useful for fixing files before they go into SharePoint but since the replacements are configuration based you could easily use it for corporate name changes or anything else where you need to do a quick set of replacements on files. If you want to try the tool send me an email and I’ll get you a copy for evaluation.