Start your tour by examining the exterior of the building. The entrance portals are done in a Byzantine style, with images from mythology, history and the Bible. The five western portals are topped with mosaics. The central one depicts the Last Judgment, but the other four tell the story of how the remains of the Apostle and Evangelist St. Mark got moved from Alexandria, Egypt, to Venice. At the time, the Muslim Turks controlled Alexandria, and the only way the Venetians could get the remains out was to pack them in a barrel full of pork products. Pork is considered forbidden and unclean by Muslims, and the Turks didn't want to get anywhere near the barrel, so they waived it through and let the Venetians load it onto a ship.
Note the four bronze horses over the entrance. These are replicas of the originals, which were stolen by Napoleon and taken to the Tuileries Palace in Paris. The originals were later returned to Venice and now reside in the St. Mark's Museum.
Enter the central door and take note of the ceiling mosaics depicting scenes from the books of Genesis and Exodus. Head to the central door into the church, but in the doorway, take the stairs to the right up to the next floor. Here you'll find the above-mentioned horses, various artifacts, a banquet room used by the various Doges (the elected dukes that ruled the city) and views into the church and out onto the Piazza. The Museum charges an entrance fee.
Descend to the ground floor and go on through the central door into the church. Because of the press of people, you'll have to move around in a counter-clockwise pattern. Over the nave is the Dome of Pentecost. The chief glories of St. Mark's are the gilded mosaics in the ceiling. The marble floor is interesting as well--it's uneven due to the shifting foundation. Work your way around to the south transept and pay for admission into the Tesoro, or Treasury, which houses religious relics and vessels as well as booty captured in battle.
Exit the Treasury and take note of the Dome of St. Leonard over the south transept. Work your way east, noting the central Dome of the Ascension. You can either go on at this point and see the rest of the church or you can pay for admission into the Sanctuary. If you take the latter course, you'll go behind the rood screen, past the Chapel of St. Clement and on to the altar and baldacchino, behind which is the Tomb of St. Mark. Beyond that, the splendid Pala d'Oro--the gold altarpiece--dominates the apse. Directly over the baldacchino is the Dome of the Religion of Christ. Move along to the north past the Chapel of St. Peter and go back out into the main part of the church.
Look for the icon of Our Lady of Nicopeia on the eastern wall of the north transept, the mosaic of the Tree of Jesse on the north wall and the Dome of St. John overhead. Move on into the nave and exit.
Cross the Piazza San Marco, the space Napoleon famously called "the finest drawing room in Europe," and go over to St. Mark's Campanile, or the bell tower. Pay to take the elevator up to the top for great views of the city and its canals.