As if aboveground Rome isn't fascinating enough, we are planning also to visit subterranean Rome, the streets, buildings and cemeteries under the city. I have tickets for the Vatican necropolis and I want to see the church of St. Clemente. Is the Domus Aurea worth seeing? Some of the underground tours available are quite expensive so we would rather go to sites on our own. Does anyone have further suggestions? We will also be visiting the catacombs.

You might look into the Crypta Balbi--a rather new addition to the underground and the Museo Nazionale d'Arte Romana. For information from our visit there go here http://www.janeandken.com/travelmemories.html and do a search for Crypta Balbi. You are right on with the Scavi tour and St.Clemente--both fantastic. The Domus Aurea is worth going to just because it is--although once there it is somewhat diappointing until you try (and try is the operative word) to envision what it might have been.

Agree that the Scavi and San Clemente should be seen but to me,the best part of being in the Domus Aurea was that it was a cool escape on an exceptionally hot day. As for catacombs, the best are San Sebastiano and San Calisto. Other underground sights to consider:
The Mamertine Prison
The ruins of St. Cecilia's home and a Roman tannery under the church of Santa Cecilia in Trastevere.
Roman homes from the 2nd and 3rd centuries under the church of Santi Giovanni e Paolo on the Celian Hill.

I think the Domus Aurea is a must! I went on a Context Rome Underground Rome tour and loved it. I think if you do a little research before you go,you'll certainly enjoy it.

The Domus Aurea doesn't seem to be very popular on this board, but I found it fascinating. Personally, I think it's worth it. Just do some reading about the history and I think you'll find it amazing.

Thanks everyone for your help. I now have enough sites to visit to satisfy my appetite for underground adventures.