Museums/monuments with entrance fees, like the Vatican Museums, can be booked in advance or you can still wait in line for a ticket. All of Rome’s churches, as well as the Pantheon, are free to enter but there are no skip-the-line services for churches in Rome.
Here is a list of the Rome’s top free sites:
Pantheon
Trevi Fountain
Spanish Steps
Piazza Navona
Largo Argentina (Teatro Pompei can be seen from street level)
Campo dei Fiori
Tiber Island
Villa Borghese
Villa Pamphili