There are a lot of great places depending on your budget. Downtown, I really like The Peninsula Grille ($100+ for two). A little less fancy but as good or better is SNOB. Fleet Landing is good and right on the water, near the cruise ships. It's more casual then the other two.
Benito's - (Mt P. - in Town Center, they may be closed or moved due to lease issues with shopping center)
The Mustard Seed (Mt. P - this is where we usually take friends who come to visit)
Benito's did close for a while but I'm pretty sure they're open now. Great Italian at good prices, service can be a little slow at times.
The Mustard Seed I believe has two, possibly three locations, in Mt. P on Bowman Road, James Island, and maybe downtown? It's good, if a little eclectic.
There is a mexican restaurant over on JI next door to the Terrace (a really cool indie theater, btw) that has fantastic food and tasty margaritas too. I can't remember the name though.
Andolini's pizza is awesome. King street brewery is really good
Andolini's is awesome - if you go to the best ones.
My experiences and impressions:
N. Charleston on Rivers - Great food and service, clean and well maintained.
James Island - Great food and service. Seats are wore out.
West Ashley - Great food and service. A little dirty.
Wentworth Downtown - The original. Sadly, I haven't been yet. When I am hungry downtown, I almost always head to Kickin' Chicken.
Mt P (where I live) - Slow service (waited over an hour on two occasions and they were not that busy; waitresses forgot about order) and the pizza is often under done. Seats are OK, some are worn. Not as clean as Rivers or JI, seems cleaner than WA. We quit going there last year and get pizza from Matt's Pizza Delivery (was NYPD New York Pizza Delivery) or drive over to James Island or West Ashley.
boulevard diner, mustard seed, sette 7 among others are owned by Sal Parco and are great.
Santi's is a great little restaurant for casual mexican food
Mellow Mushroom for a great casual pizza joint
i agree "The Wreck" is some of the best seafood around charleston, and Shem Creek bar & grill is still my "old faithful". prices have gone up but food is still great. Boathouse is an excellent choice too. Personally not a fan of Hyman's, i beleive the food is average and is more of a tourist trap than anything. you wont find many locals in there for that reason.
theres a great deli on Coleman blvd as well named Mozzo. Liberty (also in mt. pleasant) is pretty good.
Shoney's on the water... thats funny. We try to go out to eat somewhere everyweekend. I'll try some of your suggestions. Never been to Shems Creek. Maybe we'll go there this weekend. Thanks for the info.
Hands down, the best restaurant in Charleston is The Fat Hen on John's Island. Absolutely amazing casual French food with a Southern twist. Their brunch o Sundays is awesome too.
If you want Italian, check out The Wild Olive (also on John's Island), or Al Di La. Both have amazing food. You also can't go wrong with SNOB (try to sit at the chefs table) or Cypress.
Skip Hymans. Terrible fried seafood that isn't even fresh. Most overrated restaurant in Charleston . They close off dining rooms to make it look like they are busy (my wife used to work there). The owner is scum and just wants to make a buck.
So many good places I can't list them all. My favorites, in no particular order:
Sesame Burgers and Beer
Moe's Downtown (Heard good things about the crosstown on Rutledge, but it's closed temporarily for repairs)
Chai's (Very good tappas, moderately priced)
Liberty Taproom (good happy hour)
Again, there are so many good ones. I think you could eat out every night of the year at a different place and be very happy.