We stayed at the Welgelegen Guest House which is in the garden district and within walking distance to mainly everywhere except the V&A Waterfront. Actually you can walk to the V&A too but we always took taxis at night. For some reason the webpage isn't working right now but here is the tripadvisor page. We really loved it. We were there on honeymoon and they welcomed us with a bottle of champagne, strawberries and a dozen roses.
In Cape Town we ate at:
Nelson's Eye steakhouse - was ok. We did not pick it but had dinner there with friends. I found the meat sort of dry and the waiter told me it's bc of the way they age their meat.
Ocean Basket - Interesting experience. It's a chain. There are no menus. They bring you this huge chalkboard with the catch of the day. Good prices but you will find fresh seafood everywhere in Cape Town. I liked the laid back atmosphere. It was kind of like dining in your back yard.
Africa Cafe - Fantastic experience. A little touristy but there were lots of locals there for celebrations as well. It's a fixed menu with dishes from various African countries. They have a live music and dance show as well.
I don't remember where we ate lunch. I know one day we did a Cape tour (we did the winelands/Boulder Beach/Cape of Good Hope in the morning and Stellenbosch in the afternoon) and another day we ate on the V&A Waterfront.
The day tours are good if you don't want to be bothered driving around (they drive like crazy people on the highways) and want a guide to tell you info instead of reading it from a book. You spend a lot of time in the car with them so it's also a good way to get local information on the city if you want it.
Definitely go to the markets. The Green Market Sq. is a bit of a tourist trap but the market down by the aquarium has decent prices. Skip the aquarium. It's not worth it.