Hey Jules,
For me, hands down, St. Peter's Basilica is my most favorite.
While there are many beautiful churches in Rome, large and small, I was drawn to St. Peter's over and over. I never tired of it. Despite the crowding at times, it did not even faze me. There is so much history about St. Peter's. So much to see. You can spend hours in there. I got a great book about The Basilica.
I had a couple of very special experiences to add to my love for the Basilica. I attended a very special celebration Mass officiated by Pope Francis to honor Our Lady of Guadalupe - The Mass was stunning and beautiful. Priests sang many songs. I was elated to find the recording of the whole Mass on youtube. I "snapped a memory" of the whole Mass - an experience I will never forget.
Just walking up to the St. Peter's Piazza, it is amazing and awe-inspiring in itself. Plus, the added 'treat' was I was there for the beginning of the Christmas season - A gorgeous, hand sculpted Nativity - sand imported from Venezia. A huge tree that sparkled a special glow upon the Nativity. The ornaments and special dedication of the tree changes each year. I was witness to that since going two years in a row.
As you look up on the Basilica, the 140 statues of the Saints seem to give a "soft welcome with a gentle guidance" to all who enter.
When I walked in the through doors, and saw to my immediate right, La Pieta, some kind of Peace took over. It is beautiful and sad at the same time. Seeing it will invoke different emotions for people. I bought a beautiful La Pieta that is made in Italy. It was in one of the gift shops. I treasure it, and it brings me right back, so vividly, to my visits.
There is the Chapel of The Blessed Sacrament - gorgeous, ornate, peaceful, spiritual. It is a dedicated prayer, reflection and silent chapel. There is seating of course. Guards will remind all to turn off phones and cameras and any recording device.
St. Peter, The Chair of St. Peter - a real "presence." I love it.
There are a lot of altars to visit within the Basilica. Some have pews you can sit and reflect.
Two adorable chubby, marble Cherubs adorn the Holy Water font - It is usually filled with the Holy Water. If you are inclined, you can bring a little glass bottle to fill. Or, you can buy an empty one in the gift shop for 3€. I brought my own, lol.
Above the Cherubs is a statue of St. Teresa of Jesus - Order of Carmelites
Here is a link (floor plan) of St. Peter's Basilica - very easy to follow
http://stpetersbasilica.info/index.htm
I would also add that at different times I visited - morning, afternoon and evening, each was a delight to walk around the Piazza.
Nightfall was my favorite. The Nativity and Christmas Tree lit up were beautiful and lovely. Walking "away from" The Church, I turned around a few times and was just blown away - the lights around the Church with its soft "halo-like" glow, the approaching darkness, the gentle command of The Saints above - breathtaking.
Jules, if you visit, I hope you enjoy it as much as I did. I can't wait to return!