To say that there's plenty to see and do while in Rome. Fortunately, the city is very compact, and you can get to most of the sites with relative ease just by walking. We spent 2 full days in Rome and managed to get to most of the big sites without too much worry.
The Pantheon was the wife's favorite site. It's hard to disagree, as the building is just astounding. It's dome is as high as it is wide, and has been used for multiple religious activities over its existence.
I don't know that I could say what my favorite was, as there was just so much to see there. I did enjoy Hadrian's mausoleum/Castel Sant'Angelo (the castle is built around the mausoleum), as it offered a tremendous view of the city. We managed to get there after dark and saw the city as it was lit up for the evening. That said, the Colosseum and the Forum were both pretty amazing, as were the city walls. The artwork in the museums of the Vatican, including the Vexullum Regis (rumoured to have pieces of the Cross in it) were unbelievable. The detail found in the frescoes and sculptures were beyond what one might seem possible.
We didn't get to the Borghese Galleries, which is somewhat unfortunate, as I understand the artwork there is also tremendous. And we missed out on Trastevere, and most of Campo dei Fiori. But what we did see was pretty amazing. Piazza Navona was chock full of painters hawking their wares, some of it rather nice, but nothing we were going to spend money on. The fountains there were pretty interesting, though not as spectacular as Trevi Fountain. Another set of fountains that were really interesting were the Quattro Fontane, which we happened by on accident. The detail in these wall fountains were also somewhat spectacular.
It was a very interesting trip, and one that I hope to make again someday, perhaps with a little more time to move around and see things (and a little more cash, too).