OP, we went to Hilton Head in 2010, and took day trips to Charleston, SC, and it was fabulous! We didn't get to do everything we wanted, because the in-laws were with us and they both tire easily (multiple health issues for both of them), but here are the highlights:
In Charleston, we did a horse-drawn carriage tour, ate at a local BBQ restaurant, did some shopping at the city market (it was directly across the street from where we boarded our carriage tour), and took a tour of Magnolia Plantation, which was gorgeous-they have fabulous antiques, including a copy of Audobon's "Birds Of North America".
In Savannah, we did a trolley tour, which was wonderful. It took us around the various squares and highlighted the historic homes and other areas of interest-we found it very informative. We ate at The Lady & Sons, which is Paula Deen's restaurant. The food was good, not spectacular, but it had a great atmosphere and our server was wonderful. My DD16 (13yo at the time) had key lime pie for the first time, and proclaimed it delicious. We also toured the Mercer-Williams House, which is the site of the murder chronicled in the book (and movie) "Midnight In The Garden Of Good And Evil". I LOVED it! I'm a big fan of the book, though.
In Hilton Head, we went on a dolphin watching tour, and went parasailing (DH sat that one out), and we had an amazing time on both. I loved parasailing, and would do it again in a heartbeat! The beaches are gorgeous, and DD and I enjoyed looking for treasures (shells and such) while walking on the beach. There is also a great little ice cream shop and also a great Mexican restaurant over by Disney's HHI DVC resort (the name escapes me).