My favorite restaurant in Cape Town was Arnold's on Kloof Street. Nice views of Table Mountain, excellent food, and very nice people. On my last days in CPT, my friends and I had dinner there 3 nights in a row. Their specialty is mainly game meats (ostrich, springbok, crocodile, etc.)

http://www.arnolds.co.za/

I also ditto the recommendation for Haiku. Outstanding food there as well.

I found most of the restaurants on the V&A Waterfront to be overpriced and too touristy. They're not bad, per se, just too pretentious and not authentic IMO.