Ideally, you will have more than a day here. It%26#39;s such a lovely city of gardens, temples and quiet neighborhoods that 2-3 days would be best.
However, our visit was by cruise ship and we had from 8-5 to get it all done.
Here%26#39;s a link to my travel blog for a trip report with photos:
In summary: you likely know to go to the atomic memorial, peace park and museum. But there is another very cool area called Teramachi Street. Here you can visit temple after temple including their gardens, mostly for free. Public transportation is perfect for getting around, but my tip is to take a digital camera. We used it to take pictures of our tram stops and street names so as not to forget our way back.
If you are going by ship, hopefully they will have a children%26#39;s performance for you before you sail. If so, you absolutely must go. Both the dancers and the drummers we had on the pier made for the best sail away I%26#39;ve ever seen.
I hope you enjoy Nagasaki as much as we did!