Is there an annual pass that allows you to get in to all the California missions?

There is no annual pass. The missions are individual entities that set their own schedules and entry fees. Most are active catholic churches where there is no fee for entering the church for mass but where there is a fee for entering the mission grounds and completing a full tour. Entry is usually through a mission gift shop. The missions which are state parks (for example, La Purisima) also have an entrance fee.