My wife and I arrive in Rome at 8:30 am on July 15th 2009, and have until the afternoon of the 17th before boarding on a cruise at the Port of Civitavecchia. We are thinking of taking a train from the airport and staying at a hotel near the termini for the convenience of luggage handling. We would greatly appreciate any hotel suggestions as well as your thoughts on how our time can be best spent. Thanks very much.

With 3 days in Rome, I would recommend staying in a neighborhood that appeals to you, rather than one strictly for convenience. The neighborhood near the train station is fine for 1 night, but really doesn't have the charm that makes Rome so special.

My favorite neighborhood is the Trestavere neighborhood. It's an easy bus ride from the train station, and it's within walking distance of the major sites if you enjoy walking. Good luck!

Borghese Museum
Colosseum
Vatican Museums
Campo dei Fiori for breakfast and the morning market
Walk around Trastevere
Pantheon
Santa Maria Sopra Minerva
St Peter in Chains
St Peter's basilica
Bernini ecstasies in San Francisco a Ripa and Santa Maria della Vittoria
Sant'Andrea al Quirinale
St Paul Outside the Walls
Concert in the evening

jenmoore, your recommendation to stay in Trestavere sounds so much better than the termini. Any hotel suggestions for the area around 100 to 150 e per night.
Thanks

I second what Jenmoore says about staying in a neighborhood. On my trip to Rome in March we stayed at Hotel Portamaggiore and while the hotel was fine and close to the termini, it was too far removed from the areas we wanted to visit most. Much nicer to stay nearer the main sights. You still walk a lot but you see and feel more of what you're in Rome for.
If you are planning to see the Vatican, get tickets ahead of time online. Don't waste time standing in line in the heat. Pay attention to the days museums are closed and plan accordingly.
Rome is big so plan well for only 3 days. Don't cram it so full you rush through everything. My favorites were the Vatican, Piazza Navona, Campo di Fiori, and Trevi Fountain, no big surprises there. The Hop On Hop Off bus was a major disappointment, very little description, bad sound, and even parked for 20 minutes for the driver to take a break. Also the stops were not even close to the map we were given when we got our tickets. Just walk or if necessary take a taxi. We had several adventures with our taxi drivers, so be very sure to put on your safety belts. No kidding.

If you stay in Trastevere, you can take a local train from the airport instead of the Leonard Express which goes to Termini. You can also catch the train to Civitavecchia at the Trastevere station. For hotel in Trastevere, you might try the Arco del Lauro.
http://www.arcodellauro.it/index.php?lang=en

adrienne, great list, thanks

Challiman & kybourbon, thanks very much

Here's one in Trastevere. July prices are less than what's on the web site. They also have apartments. I prefer Trastevere but many people also like Campo dei Fiore or Piazza Navona area.

http://www.hoteltrastevere.net/en/index.html

I stayed at Hotel Santa Maria in Trestavere and absolutley loved it: http://www.htlsantamaria.com/

The rooms are small but comfortable, there's a lovely garden to sit in and the general feel is very welcoming and charming. They even have bicycles you're invited to borrow.

Have fun!

kybourbon,Trastevere looks and sound good for a train access comming into from the airport and leaving to go to the port.The hotel arco del Lauro did not have a room, they were however very nice . Do you have another recomennded room for the 2 nights or should we consider staying in the Piazza Navona or Campo del Fiore area, if so a holtel name would be great. It looks like we can walk everywher from that area.
Thank you agaain and again for your patience and assistance.