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I stayed at Atlantic Point Backpackers in Green Point. Nice place. Short walk to the Waterfront. Took their Cape Peninsula tour, which included the Boulder Beach penguins - I think it was via Backpacker Bus (there's another company that runs the same tour, but I forget its name). At the time, Robben Island tours were selling out. I kept watch on their web site for days without sell-outs and was able to walk down to the harbour and snag a ticket.

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I stayed at Long Street Backpackers and would recommend it. You can't get more central than that.

You have to book Robben Island in advance as it does sell out. Not sure if you could combine it with a tour to Cape of GH in a day. Maybe consider hiring a car for one for this?

You could do the shorter of the hop on/off tours in half a day. Not sure if it is worth doing both, but you should try get out to the Winelands.

Regarding Table Mountain, if you are going to hike up, maybe the morning would be better than afternoon, as it could get pretty hot.

Try and get on a tour out to do shark diving, it's well worth it.

Not sure how to fit all the above into an itinerary, but you will be able to figure out a lot once you get there. If I was to drop one thing, it would be the hop on/off bus.

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Shark diving is at 2 destinations, Gansbaai which is about a 2 hour drive from CT pick up is about 6am or at Simon's Town which is less than an hour from central CT, you could afterwards go to Boulders & Cape Point via the green bus but it's much better if you drive yourself then head over Chapman's Peak Drive for sunset & onwards to Camp's Bay (which you should like). Table Mountain, head up hear as soon as it's clear of clouds & also pop across to Signal Hill. The blue HOHO route wine tour is nothing compared to what you can get at Stellenbosch & Franschhoek look for a tour to here. I think this blue HOHO bus route goes as far as Tokai which is not far from False Bay & therefore you could end up going out this way twice when short of time.

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ashanti gardens is a great place to stay at. http://www.ashanti.co.za/ in the "main lodge" there is a travel centre (where you could your day tours), a bar, restaurant, garden and a courtyard with a small pool. accommodation here is mainly in clean dorms. just around the corner (a minute walk away) the have two guesthouses, with nice doubles with attached bath and very reasonable prices. if you stay in one of the guesthouses, you can also use the facilities of the main lodge.

your plan is really good, my suggestions:
1 day hop-on / hop-off bus (red route) - a great way to see the main attractions of the city, with commentary, to get your bearings, to hop-off where you like it (and not hop-off where you dont like it :-)). the red route includes camps bay and clifton, so you can combine city and beaches.

for the winelands, i wouldnt go on the blue hop-on / hop-off bus, but instead on a day tour to the winelands. the travel centre a ashanti (or any other travel centre / hostel reception) can book you a day tour.

a day tour to the cape peninsula is also a must. all companies pretty much have the same itinerary, so i dont think it matters which one you choose - again, book at the hostel.

for your free half day, i think it really depends on your interests, and also on the weather.
the aquarium at the v&a waterfront has some really lovely tanks, and would be my favourite on a rainy day.
if you like nature / flowers / parks, and the weather is good, kirstenbosch botanical garden is absolutely beautiful.
if you are interested to learn a little bit more about the not so far away history of south africa, visit robben island (get to the robben island gateway on the v&a in the early morning or better still, book ahead).
or - you dont have a "sight in mind", and just walk around and explore & shop. at the v&a waterfront, the fleamarket on greenmarket square, in de waterkant or around gardens.

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Thank you all SO much for the information!! It was VERY helpful.

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Thank you for all that great information! The Ashanti Hotel looks great, did you find the location worked well? It seems a bit out of the way, but did you find this was a problem?

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the ashanti is in gardens, for me one of the best areas to stay in cape town. plenty of restaurants, bars, cafés, shops in easy and safe walking distance. i definitely prefer to stay in gardens than in the central business district / and along lower long street - fine on working days untill 5pm, but on weekends and in the evening is does sometimes get a bit dodgy (at least I didnt feel comfortable there on my own, and never had that problem in gardens). the red bus route has a stop very close to the ashanti (infront of the mount nelson hotel). you can walk to the waterfront in about 30 minutes.

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Thank you very much for your response! I went with them :)

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Anywhere in Long Street...there is a HUGE choice...