Magnolia Plantation and Middleton Place are well worth the visit. Charleston itself is great to just walk around and soak up the old atmosphere. There are a few of the old homes that you can pay for a tour, I forget their names now but they'd be mentioned in almost any tour book...
Stay in the middle of town if you can. Highly recommend the French Quarter Inn, its in a fantastic location, the rooms are great and the free wine/cheese in the evenings is a nice touch.
For home tours, you can buy a 2 day pass that will get you into a lot of good locations. The best is probably Drayton Hall outside of town. It's probably the finest example in America of preservationist architecture. (Not restoration but preservation.) The house is still in very good condition and hasn't changed at all since the 1700's. (No electric or running water.)
You might also take one of those horse drawn carriage rides. They can be pretty informative.
As for restaurants, I'll recommend two but there are tons of good restaurants there. First, go have breakfast at the Hominy Grill and order shrimp and cheese grits. I've been eating there for years and then I saw GQ magazine rated in the best breakfast in the the country. It's easy to see why.
The second would be Slightly North of Broad or S.N.O.B. I had one of the best steak dinners in my life there and I'm a steak snob. Very good good food and great atmosphere.
I have stayed at Middleton Place and also at the Harborview Inn. They serve a roof-top breakfast at the Harborview with a nice view of... the harbor. Middleton Place is a quite laid back place to stay on an old planation that is a few miles north of town, just down the road from Drayton Hall.
No visit to Charleston is complete without a visit to Fort Sumter in Charleston Harbor. You can take a ferry boat out to it from Patriot Point next to the USS Hornet.
Try Mimi's for breakfast. It is about 5 miles north of downtown Charleston.
My favorite beach is Holly Beach. I just like the feel of the place.
Coast was good last time I went.