A customer's MOSS implementation stopped sending alerts after items were being updated. If someone was to sign up for an alert they would get the initial email but then after that no more alerts.

If you look in Central Administration and go to Operations then Timer Job Status, you should see a job Immediate Alerts for your website url. If you do not, the timer job was removed. Don't ask my how it was removed, good luck finding that out!

Anyway, run these two easy commands and you'll be back up and running, er, alerting.

stsadm.exe -o setproperty -url http://mysite.mydomain.com/ -pn alerts-enabled
-pv true

stsadm.exe -o setproperty -url http: http://mysite.mydomain.com/ -pn
job-immediate-alerts -pv "every 5 minutes"

Hope this helps!