I was able to fix this problem for one of my users but I don't think it applies to the OP since his problems are fixed with a reboot. However it may be relevant to some of the other posters with a similar problem.
A user of mine was having the same problem with being unable to open files when double clicked from the Finder. The appropriate application would open, but to a blank document, not the file selected. Using File > Open from within the application worked fine.
Originally I thought this was a symptom of the email client mishandling the file type since the first file we saw this behavior with was a downloaded email attachment (attachment issue discussed here:
http://www.officeformac.com/ProductForums/Office/1973/).
After examining the file types of several of the affected documents, it was clear that was not the issue. After some trial and error, I figured it had to be a problem with the file path. Turns out, every affected file was contained in a folder or had a file name that contained the # character. Removing the # allowed the file to be open with a double click.
This behavior only occurred after upgrading to 10.6 and it only seems to have a problem with the # character but it's conceivable this problem could occur with other non alpha-numeric characters contained in your file path. All files I had the issue with were Office 2004 documents.
Hope this helps someone.