High Priority Sites
Capitoline Museums: The museum is divided between the Palazzo Dei Conservatori and the Palazzo Nuovo. An overview is provided by Wikipedia. Likely open from 9 am - 8 pm, Tues-Sun.
Colosseum: For an overview, see Wikipedia. The Explore Italian Culture web-site has a section on Roman Colosseum -- How To See The Secret Parts.
Palatine Hill: Wikipedia has an overview of the historic hill. The Villa Di Livia may be the most impressive site on the hill. Wikipedia offers a brief introduction to the Villa of Livia. The House of Augustus is also described by Wikipedia. One ticket includes entry to the Palatine Museum, the House of Livia, the Roman Forum and the Colosseum.
Roman Forum: An introduction is provided by Wikipedia.
Ara Pacis: See Wikipedia for a brief description.
Pantheon: For a detailed introduction, see Wikipedia.
Vatican Museums: The Vatican Museums has an On-Line Ticket Office. There are special Night Openings of the Vatican Museums. See Wikipedia for a description of the museums.
Saint Peter's Basilica: Wikipedia offers a full description. Open 8 am - 5:45 pm daily. The pre-Constantinian necropolis can by visited by appointment or visit the Excavations Office on the right of the colonnade. Public audience with the Pope is usually Wed. at 10:30 am and in the Piazza on Sunday at Noon.
Other Starred Sites
Villa Giulia: Described as Italy's most important museum of Etruscan Civilization. Wikipedia provides an introduction to the museum. Open 8:30 am - 7:30 pm, Tues.-Sun.
Santa Maria In Araceoli: See Wikipedia for an overview.
Time Elevator: An experiential filmed introduction to the history of Rome.
Appia Antica Park: The road starts at Porta San Sebastiano. The beginning of the Appian Way is closed to traffic on Sundays. Wikipedia has an overview. See Rick Steves, "Time Travel On Rome's Ancient Appian Way," San Francisco Gate, July 12, 2012.
Museo Nazionale: Wikipedia has an overview of this multi-branch Rome museum. Lonely Planet includes a brief description of the Palazzo Massimo Alle Terme. See Tripadvisor on Palazzo Altemps, another branch of the museum. One ticket gives entry to the five branches.
Monte Testaccio: Rome's mountain of pot shards. See Wikipedia for a description. Open by appointment only (tel: 06-0608).
Circus Maximus: For an introduction, see Wikipedia.
Underground Rome
Ancient City Underneath: Reid's Italy has some useful information.
Le Domus Romane Di Palazzo Valentini: A well-reviewed villa under the streets of Rome. Revealed Rome includes a description and ticketing information. TicketOne has ticket ordering information.
Church Of San Clemente: This church reveals layers of history from pagan temple to 15th-century church. For an overview, see Wikipedia. Open 9 am - 12:30 pm, 3-6 pm, Mon-Sat. Check for the catacomb as well as the layers.
Santi Giovanni E Paola: A number of houses are located beneath this church. See Wiki's Churches Of Rome. A brief introduction is provided by Wikipedia. Open 10 am - 1 pm, 3-6 pm.
Sotteranei di San Paolo Alla Regola: An old palace hides the remains of an ancient Roman house. DK includes brief details about this subterranean site. A ramp lead down well below today's street level (Tel: 06-0608). Open by appointment only.
Catacombs: A very brief introduction is provided at the Official Rome Tourism site. A more thorough overview is at Wikipedia. The Catacombs Of Domitilla are recommended by different sources. Open Wed.-Mon., 9 am - Noon, 2-5 pm.
Santa Maria Della Concezione Dei Cappuccini -- Wikipedia: Atlas Obscura offers a good introduction. See also Capuchin Crypt -- Wikipedia: and Cemetery Of The Week #15 -- The Capuchin Catacomb Of Rome . The official web-page of the Capuchins is located here.
San Nicole In Carcere: Wikipedia has a brief description. See also Revealed Rome.
Church Of Santa Cecilia: See TripAdvisor for some comments.
Rome Sotteraneo: A group that organizes more ambitious underground tours.
Underground Rome For Families: A tour that may provide some ideas for our own exploring.
Underground Rome Tours: Another tour company to use as reference.
Other Possible Sites
Galleria Borghese: For an overview, see Wikipedia.
Sacred Area Of Largo Argentina: Includes the spot at which Julius Caesar was assassinated.
Mamertine Prison: According to tradition, Peter and Paul were imprisoned here. See Wikipedia for an introduction.
Trajan's Column: The centerpiece of Trajan's Forum. For a detailed description, see Wikipedia.
Basilica Of Santa Maria Del Popolo:
Basilica Santa Croce In Gerusalemme: Includes frescoes depicting St. Helena's discovery of the True Cross and a statue of Juno converted into Constantine's mother. For an overview, see Wikipedia.
Scala Sancta: An introduction to the site is provided by Wikipedia. Hours are highlighted at the official site.
San Pietro In Vincoli: See Wikipedia for an overview. Sacred Destinations has a brief description. Highlights include the chains of Peter below the high altar and Michelangelo's Tomb of Pope Julius II. Open 8 am - 12:30 pm, 3-7 pm.
Insula: This Wikipedia overview includes mention of the Insula open to public viewing in Rome.
Touring Information
Soprintendenza Speciale Per I Beni Archeologici Di Roma: A government site that offers much information about historic monuments.
Through Eternity Tours: This includes a brief underground tour.
Transportation
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Useful Websites
Miscellaneous
Ella Morton, "Gladiator School: Where You Can Fight Like An Ancient Roman," Slate, December 20, 2013.
Fabiana Formica, "Gladiator School: When In Rome, Fight Like A Roman," Atlas Obscura, December 13, 2013.
Museum Of Roman Civilization: This is presently closed for renovation.
Other Accommodations
Between Colosseum And Trevi Fountain: .
Great Beauty -- The Colosseum: (Via Ostilia, 1/A; +39 3351 041 358)
Nice Home Near Forum And Colosseum: (Via Baccina, 15 Via Baccina 15 int. 2; +39 3397 350 487)