I realize this is a bit like comparing apples to oranges but we only have 3 days and can't do both. Let the debate begin. We're both Rome sophmores if that helps. We'll be there mid March, 2012.
I'd vote for Ostia Antica. It's a huge site, with remains of three and four-story buildings that were apartment houses, plus the usual temples and a wonderful market place where all the trade associations had their mosaic "logos" set in the pavement. Almost nobody was there when we toured it before Easter a couple of years ago. Our biggest problem in a car was finding the entrance: huge signs on the highway, but only a tiny gate with a little sign facing it, not the road, on a back street.
Ron in Rome has excellent info that could help you to decide. Here's his page on the catacombs of Rome and his take on Ostia Antica. You can't really go wrong with either one, so don't sweat it too much. Happy travels.
If you have not visited Pompeii then OA provides a large open expanse of an ancient Roman city, as does Pompeii. Well worth the short trip. If you have visited Pompeii then OA still is worth it, but for me Pompeii 's in-tact houses, frescos, body castings and sheer size, literally under Vesuvius, make it the gold standard; but there is a healthy informed debate about this. If you are dying to see a Roman aqueduct (I was) then the Appia Antica Park http://www.parcoappiaantica.it/it/index.asp is it. Great photo ops. The park, which is many square miles, includes portions of the ancient Appia Amtica, some interesting restaurants and a few famous catacombs plus miles of hiking and biking routes. It is not obvious how to access all of this so if you decide to go there you might benifit from posting a question here. I've done the catacombs. An interesting one hour event that I did just to check it off the list.
I agree w/ the above reply, you will find either side trip interesting and worthwhile, although I would lean towards seeing the catacombs if you are 'religious' and interested in learning about how the early Christians worshipped.
Ostia Antica is very worthwhile, especially if you don't have time for Pompeii, however, unlike one of the above replies, I would skip OA if you have visited the ruins at Pompeii (especially if you're short on time).
Thanks for the good advice everyone. We have been to Pompeii so perhaps Ostia Antica isn't for us this trip. We have 3 days in Rome. We are also considering Hadrian's Villa and Tivoli, both of which look amazing.