St. Peter's church is definitely awe-inspiring. Now out from under the scaffolding that covered it's facade on my first trip in 1998, the church is the high point of Rome - literally. (A city ordinance makes it illegal to build any structure taller than the dome of St. Peter's.)
Enter the church and find the burgundy colord marble circle near the rear of the church. Stand here (on the spot where Charlemagne was coronated) and survey the immensity of the building. Imagine what it might look like had the architech's original design prevailed - a symmetrical Greek cross with a center dome rather than the Latin cross design that was actually built. The nave (center aisle) would only be half as long!
To your right (behind bullet proof glass - some crazy guy attacked the statue with a hammer in the late 70s) is Michelangelo's Pieta. Straight ahead in the center of the church is Bernini's canopy. St. Peter himself is said to be buried underneath. Rub the foot of the statue of St. Peter (on the right before you reach the canopy) for good luck. (This statue is the only remaining item from the original St. Peter's church.) Survey Raphaello's "paintings" on the walls, which if you look at closely you will notice are not actually paintings at all but mosaics.
See everything you want to see in the church, then decend the stairs into the crypt housing the bodies of many of the deceased popes. Make sure you visit the crypt last, as the exit leads outside the church.