A great all-day breakfast place with a twist is 
Signe’s Heaven Bound Bakery & Café (93 Arrow Rd., 843/785-9118, www.signesbakery.com [1], Mon.–Fri. 8 a.m.–4 p.m., Sat. 9 a.m.–2 p.m., $5–10). The breakfast comprises tasty dishes like frittatas and breakfast polenta, while the twist is the extensive artisan bakery, with delicious specialties like the signature key lime pound cake. You’ll be surprised at the quality of the food for the low prices. Expect a wait in line at the counter during peak periods.
There are a couple of great diner-style places on the island. Though known more for its hamburgers and Philly cheesesteaks, Harold’s Diner (641 William Hilton Pkwy., 843/842-9292, Mon.–Sat. 7 a.m.–3 p.m., $4–6) has great pancakes as well as its trademark brand of hilariously sarcastic service. Unpretentious and authentic in a place where those two adjectives are rarely used, Harold’s is one of a few must-visit restaurants on Hilton Head [2]. As one patron has said, “The lack of atmosphere is the atmosphere.”
You’ll find another great locally owned breakfast spot at Skillets (1 N. Forest Beach Dr., 843/785-3131, www.skilletscafe.com [3], breakfast daily 7 a.m.–5 p.m., dinner daily 5–10 p.m., $5–23) in Coligny Plaza in the Forest Beach area. Their eponymous stock in trade is a layered breakfast dish of sautéed ingredients served in a porcelain skillet, like the “Kitchen Sink” (pancakes ringed with potatoes, sausage, and bacon, topped with two poached eggs). The lunches are good too, including, believe it or not, an excellent meatloaf. Dinner is surprisingly upscale; try any of the excellent seafood dishes, like the blackened shrimp and scallops with tasso ham and blue cheese.
Links:
[1] http://www.signesbakery.com
[2] http://www.moon.com/destinations/south-carolina/beaufort-and-the-lowcountry/hilton-head-island
[3] http://www.skilletscafe.com