Vatican City

St. Peter's Square

St. Peter's Basilica (Nave)

St. Peter's Basilica (Dome)

We also visited the Vatican Necropolis, no pictures allowed

but more information can be found here, including how to book a tour:

Ufficio Scavi

Vatican Museums 

Rome, Italy

St. Angelo Castle and Bridge


Piazza del Popolo

Piazza di Spagna

Pantheon

Piazza Navona 

Fontana di Trevi

St. Ignazio de Loyola


Largo di Torre Argentina

Sta. Maria Maggiore


St. Pietro in Vincoli

Porta Maggiore and Baker's Tomb

Santa Maria del Trastevere

Santa Cecilia del Trastevere

This church has a small but very interesting catacomb which is accessible for a very small fee and is the only catacomb where photography is allowed. Access to the crypt is though the catacomb. 

Tiber Island

Bocca della Verita, Square and St. Maria in Cosmedin

Orange Garden and St. Sabina

Sto. Stefano Rotondo

St. Giovanni in Laterano & Scala Sancta

Victor Emmanuel II National Monument

Campidoglio, Capitoline Wolf & Ara Coelis

Colosseum

Palatino & Circo Massimo

Foro

Via Appia Antica

St. Sebastian

Extremely interesting tour of the catacombs here, highly recommended.
No pictures allowed.
(I personally enjoyed it more than the Vatican Necropolis)

Quo Vadis