We spent the afternoon at Doctor's Cave Beach. The taxi ride there from the pier was $5 per person, and it was $6 per person to go on the beach. The water was beautiful (cold) and we thoroughly enjoyed this $11 excursion.
The island tour we took included 4 stops: Pedro St. James, Rum Cake Factory, Hell, and Seven Mile Beach. Our tour guide (I forget his name) was extremely nice and was happy to be honest with us. I didn't feel like he wanted any pity like I've seen at other ports on tours. We got a flat tire in Hell (yes, we were stuck in Hell). Even with the flat tire, we still had an excellent time and felt like this was worth the $50 per person for approximately 4 1/2 hours.
We originally planned on going to the Mayan Ruins, but that was cancelled due to bad weather. Having been to this port multiple times before, we just decided to spend the afternoon on the ship and not get hassled by store owners.