The catacombs in Rabat are modest compared to those in Italy or France. Maybe it's the lack of stacks upon stacks of burial remains artfully arranged? Regardless, both of these sites are well presented and the tour guides do a great job.

The St. Paul Catacombs are named after the nearby St. Paul's Grotto (where the author spent several weeks after being shipwrecked). The catacombs date to the fifth century. There is an endless supply of burial troughs and the guide will explain the numerous types- there are about 10. Make sure you take the tour; there aren't any signs so you won't get much from just browsing on your own. There is an "Agape" table hewn in the rock, likely used for funerals.

St. Agatha's is a few minutes away, and contains an altar with the original colorful frescoes from the 1300's. This site is quite stunning.

It may get a tad repetitive to visit both though I wouldn't recommend one over the other.