I will be traveling to Greece in September. I have several pre-booked tours with my package but don't want to miss any "must sees" that are so often not in tra vel guides. It is a land/cruise package and below is the amount of time I will have at each place. Any tips will be appreciated.

Athens: I have one full day in Athens in addition to a day of sightseeing that includes: Tomb of Unknown Soldier, Panathenian, Temple of Zeus and Acropolis. What should I do on my second day there?

Patmos: I will have about 5 hours.

Rhodes: I will have 12 hours.

Crete: I will have 5 hours.

Santorini: I will have 5 hours.

Thank you!

Athens..a

Archeological Museum is a must see and also new acropolis museum.

Have you booked these tours with the cruise ship already or are you looking for things to do rather than the cruise ship tours?
There is lots to do in Athens. You can buy a pass that gets you into several sites many more than the ones you named in your post.
You will want to spend time in the Plaka area taking in the atmosphere and dining. Also there are lots of museums.
On Rhodes we had met another couple on the cruise ship and we went together and rented a taxi and driver for the day. We actually saw much more than the people on the ships tour and it was actually a bit cheaper too.
On Patmos the big attraction is St Johns Monastery. We chose not to take the ship tour and just wandered around the town. Same for Santorini. No need for a tour there. Santorini is all about the caldera view so just stay in town and enjoy.
In Crete you will probably want to go see Knossos. It is about 7km form the port so just grab a cab and go see it. The museum is closed.
Near the port there are some Venetian buildings that are worth looking for. Again there is no reason to take the ships tour especially if you find other people to share costs.
Here are some Athens pictures to show you what is there.
http://travel.webshots.com/album/570719132pdjjHG

For the three 5-hour layovers you really won't have much time to do anything other than take the ship's tours. Otherwise you won't even be allowed off the ship until all those passengers who take the ship's tours are disembarked. This will cut into your time ashore by at least 1 hour, perhaps more, depending on how many other ships are trying to move their passengers on or off the ship at the same time. There are only a limited number of tenders.

While Brotherlee is quite correct our experience was that by not taking the ship tours we were last priority to get off the ship. While that did eat into our 5 hours we felt we still had lots of time on Patmos and Santorini just to wander around the town and take it all in.

I havent booked any tours yet. I was waiting to hear back from people to see what they advised. In the past I've found that lots of time, exploring on my own is much more fun. However, with such limited time, I hate to miss a "must see".