If I were you, I'd make a bootable backup of your entire system before you update anything; you should never be flying blind, thinking the worst possible event can't happen to you. It will, and at the worst possible time.
Once you've done that, download and install the
10.4.11 Combo Update PPC (assuming you have a PPC Mac mini). Then use Software Update to bring your system current. Repair Permissions both before and after you do this.
In the meantime, repair permissions on your system, as well as rebuild your Mail index like this:
1. Quit Mail if it's running.
2. Go to ~/Library/Mail and delete the Envelope Index file(s).
3. Restart Mail and wait for it to import your existing messages; then check to see if any of those links will work again, without causing Mail to freeze or crash.
Mulder