Akrotiri has been open only intermittently since the protective roof over the site collapsed in 2005. If even part of Akrotiri is open, go. If the entire site is closed when you want to visit, there's no point in coming here: Unlike many sites, Akrotiri is not visible from the road.
Since excavations began in 1967, this site has presented the world with a fascinating look at life in the Minoan period. Akrotiri -- sometimes nicknamed the "Minoan Pompeii" -- was frozen in time sometime between 1600 and 1500 B.C. by a cataclysmic eruption of the island's volcano. Many scholars think that this powerful explosion destroyed the Minoan civilization on Crete. Pots and tools still lie where their owners left them before abandoning the town; the absence of human remains indicates that the residents had ample warning of the town's destruction.
You enter the Akrotiri site along the ancient town's main street, on either side of which are the stores or warehouses of the ancient commercial city. Pithoi (large earthen jars) found here contained traces of olive oil, fish, and onion. In order to get the best sense of the scale and urban nature of this town, you should go to the triangular plaza, near the exit, where you'll see two-story buildings and a spacious gathering place. Imagine yourself 3,000 years ago, leaning over a balcony and spying on the passersby. As you walk along the path through town, look for the descriptive plaques in four languages. A few poor reproductions of the magnificent wall paintings are here; the best frescoes were taken to the National Archaeological Museum in Athens, although Santorini continues to agitate for their return. For now, you can see some originals in the Museum of Prehistoric Thira and a splendid re-creation in the Thira Foundation. As you leave the site, you may notice a cluster of flowers beside one of the ancient walls. This marks the burial spot of Akrotiri's excavator, Professor S. Marinatos, who died in a fall at Akrotiri. Allow at least an hour here.