Heraklion Archaeological Museum (map). Houses the most important and representative finds from Minoan civilisation and excavations across the island of Crete. Highlights include statues of the Snake Goddess, the Bull-Leaping Fresco, the Phaistos Disk, and Minoan seals and jewellery. Also includes a number of finds from Classical Greek and Roman periods.
*Palace of Knossos (map). If you see just one ruin on Crete, see Knossos. The site is fairly compact, and much of it is accessible with restricted mobility. But 30 minutes will do it.
Within reach of a day-trip, but worth longer, are Rethymno (map), *Chania (the most charming old town on the island, map), and *Agios Nikolaos (map). Chania is the best base for exploring the *Samaria Gorge (map), and *Agios Nikolaos is your base for seeing Spinalonga (map).