Well you'll want to do the Blue Hole again, to see how the area has changed now that the Azure Window fell down. Also the Inland Sea of course while you are there.
Your dive guides will advise you - the sea conditions will vary around the island, so they will pick where the sea is safest.
You must try and do the Cathedral (underwater cave that surfaces and has light coming through holes in the rocks - breathtaking). Raz il Hobz is an underwater rock that gets a lot of sea life congregating around it.
There's also a few shallow bays where the sea life is interesting - we saw rays in one, that are good for a second dive of the day.
What else depends on your depth qualification - a lot of the wrecks are quite deep - we can only go to 30 metres and a few are around 40 - we dived over one (kalamera?) and could see it but it was a few metres below, and those with the depth qualification went inside and swam up the stairs.
Comino (the little island between Malta and Gozo) is always worth the extra cost, but I don't know if you'll want to be out all day and also don't know if they still go in the winter. There's a few sites there but the classic combo for a day trip is the wreck at 20 metres and the Santa Maria caves.
We wanted to do the Xlendi tunnel, but our guides didn't seem keen - they said it wasn't all that and the sea wasn't clean over there, but we did loads of other great dives so not an issue.