I just wanted to put out an entry for anyone with this problem. This
happened to one of my users and I could not find ANY solution on the
web/groups anywhere! Many people with the problem, but nobody bothered
to post a solution if they fixed it.
Here's what I did...

This seems to be user specific, so all you need to do is delete a
registry key:
HKCU/Software/Microsoft/Office/9.0/Excel/Options
Create a new, empty, key called "Options" to replace it.

(As always, Back up your registry first!!!)

I tried uninstalling/reinstalling (even deleting all folders for Office
before reinstall). None of these worked because Office uninstall
doesn't remove registry keys it thinks you may need again later (like
your preferences)...
Once I deleted the Options key (and recreated an empty one) the
Tools-Options dialog came back!

I hope this helps others with this problem!

ciao!