Off-beat things to do in Istanbul

I posted a reply to this, appears to have been deleted - no idea why.

Without knowing what you saw on your previous trip (top touristy things is a little vague - I'm presuming you meant the Cistern, the Blue and Süleymaniye Mosques, Topkapi Palace, Chora Church and the Archaeological museums) -
my favourites
Bosphorus cruise up to the black sea end (you actually stop just short, but can walk up to the castle on the hill for a decent view.
Islamic museum of Science
walking the old walls of Constantinople
Ferry trip from Eminonou across to Kadakoy. Particularly at sunset.

I can't imagine you could have hit everything in only three days given how large Istanbul is (I spent almost three weeks there and still didn't see everything I wanted to). Go up the Bosphorus and check out neighborhoods there, or take a ferry over to Eyup to see one of the oldest mosques (along the Golden Horn) or the Asia side (there are great food markets in Kadikoy). Go to the Istanbul Modern and Sakip Sabanci Museum and Dolmabahnce Palace. Check out Beyoglu and the New City/Istiklal Cadessi. Or take a ferry to the south and see the Princes Islands. Get out of Sultanahmet (the main tourist quarter) and there are countless things to see in every direction (you'll find mostly locals there, and hardly any tourists). Check out the Timeout Istanbul book or Lonely Planet.

I would look at TripAdvisor and find a good food tour. They generally stay away from the main tourist areas and focus more on the sidestreet places with fantastic food. Also, explore the Asian side of town. The Kadikoy area is really fun. Also, just pick a different part of town to stay in than your previous trip. You base of operations can have a huge effect on what you experience. I'm heading to Istanbul for the third time and still feel like there is tons to explore.