One of my older Zen clients is experiencing this same issue. They have an older version store (1.2.7) which had started breaking after they moved hosting a couple of times. In their case I am starting by backing up the database and running repairs, to see if there are any instances of data issues there that might be remedied.
If anyone has additional advice on what files to look at, I would appreciate it. In this site's case, all of the categories seem to be displaying the "no products to list" message, although there are products in the database for these categories. The featured and special products still display and you can arrive at those products pages in that way only.
If I have any progress I will post info here. We have been hired to try and help them fix their current site but if I cannot do so soon I may just recommend a rebuild in 1.3...




