Travel agencies arrange excursions from Iraklion to nearly every point of interest on Crete, such as Samaria Gorge in the far southwest. In that sense, Iraklion can be used as the home base for touring Crete. If you have only 1 extra day on Crete, I recommend the following trip.
Gortyna, Phaestos, Ayia Triadha & Matala
If you have an interest in history and archaeology, and you've already seen Knossos and Iraklion's museum, this is the trip to make. The distance isn't that great -- a round-trip of about 165km (100 miles) -- but you'd want a full day to take it all in. A taxi or guided tour is advisable, if you haven't rented a car. Bus schedules won't allow you to fit in all the stops. (You can stay, of course, at one of the hotels on the south coast, but they're usually booked long in advance of high season.)
The road south takes you up and across the mountainous spine of central Crete. At about 40km (25 miles), you'll leave behind the Sea of Crete (to the north) and see the Libyan Sea to the south. You then descend onto the Messara, the largest plain on Crete (about 32km/20 miles x 5km/3 miles) and a major agricultural center. At about 45km (28 miles), you'll see on your right the remains of Gortyna; many more remnants lie scattered in the fields off to the left. Gortyna (or Gortyn or Gortys) first emerged as a center of the Dorian Greeks who moved to Crete after the end of the Minoan civilization. By 500 B.C., they had advanced enough to inscribe a code of law into stone. The stones were found in the late 19th century and reassembled here, where you can see this unique -- and to scholars, invaluable -- document testifying to the legal and social arrangements of this society.
After the Romans took over Crete (67 B.C.), Gortyna enjoyed another period of glory when it served as the capital of Roman Crete and Cyrenaica (Libya). Roman structures -- temples, a stadium, and more -- litter the fields to the left. On the right, along with the Code of Gortyna, you'll see a Hellenistic Odeon, or theater, as well as the remains of the Basilica of Ayios Titos (admission 5€; daily 8am-7pm high season, reduced hours off season). Paul commissioned Titos (Titus) to lead the first Christians on Crete. The church, begun in the 6th century, was later enlarged.
Proceed down the road another 15km (10 miles), turn left at the sign for Phaestos, and ascend to the ridge where the palace of Phaestos sits in all its splendor (admission 6€; daily 8am-7pm high season, reduced hours off-season). Scholars consider this the second most powerful Minoan center; many visitors appreciate its setting on a prow of land that seems to float between the plain and the sky. Italians began to excavate Phaestos soon after Evans began at Knossos, but they decided to leave the remains much as they found them. The ceremonial staircase is as awesome as it must have been to the ancients, while the great court remains one of the most resonant public spaces anywhere. You can have a meal at the restaurant on the terrace overlooking the site.
Leaving Phaestos, continue down the main road 4km (2 1/2 miles) and turn left onto a side road. Park here and make your way to pay your respects to a Minoan minipalace complex known as Ayia Triadha. To this day, scholars aren't certain exactly what it was -- something between a satellite of Phaestos and a semi-independent palace. Several of the most impressive artifacts in the Iraklion Museum, including the painted sarcophagus (on the second floor), were found here.
Back on the road, follow the signs to Kamilari and then Pitsidia. Now you've earned your rest and swim, and at no ordinary place: the nearby beach at Matala. It's a cove enclosed by bluffs of age-old packed earth. Explorers found chambers, some with "bunk beds" that probably date back to the Romans (most likely no earlier than A.D. 100). Cretans long used them as summer homes, the German soldiers used them as storerooms during World War II, and hippies took them over in the 1960s. You can visit during the day; otherwise, they are off limits. Matala has become one more overcrowded beach in peak season, so after a dip, make your way back to Iraklion (via Mires, so you avoid the turnoff to Ayia Triadha and Phaestos).
Here's an excursion that combines some spectacular scenery, a major mythological site, and an extraordinary view on a windy day. Long promoted as "the plain of 10,000 windmills," alas, the Lasithi Plain can no longer really boast of this: The many hundreds, if not thousands, of white-sailcloth-clad windmills have largely been replaced by gasoline-powered generator windmills (and wooden or metal vanes), but it is still an impressive sight as you come over the ridge to see these windmills turning.
What they are doing is pumping water to irrigate the crops that fill the entire plain: no buildings are allowed on this large plateau (some 40 sq. km/15 sq. miles) because its rich alluvial soil (washed down from the surrounding mountains) is ideal for cultivating potatoes and other crops. Having come this far -- the plain is some 56km (35 miles) from Iraklion -- you must go the next 16km (10 miles) to visit one of the major mythological sites of all Greece: the Dhiktaion Cave, regarded since ancient times as the birthplace of Zeus and the cave where he was hidden so that his father, Cronus, could not devour him.
Driving around the outer edge of the plain (via Tzermiadhes, Drasi, Ayios Constantinos, and Ayios Georgiios), you come to the village of Psykhro on the slopes on the southern edge of the plain. Psykhro and the cave are geared for tourists who come from all over the world (admission 4€). After you reach the tourist pavilion, you still face a steep climb to the cave; you are advised to take on one of the guides because the descent into the cave can be slippery and tricky (it's best to wear rubber-soled, sturdy footwear), and you will not know what you are looking at. Although long known as the cave associated with Zeus -- it appears in numerous ancient myths and texts -- it was not excavated until 1900, and successive "digs" in the decades since have turned up countless artifacts, confirming that it was visited as a sacred shrine for centuries. Other caves on Crete and elsewhere claim the honor of Zeus's birthplace, but the Dhiktaion Cave seems to have won out, and having visited it, you can claim to have been at one of the more storied sites of the ancient world.
Lasithi Platin can also be visited as a side trip from Ayios Nikolaos. You head back westward on the old road to Iraklion and, at about 8km (5 miles), turn left (signed DRASI); then climb another 25km (15 miles) up to the plain.
Note: This information was accurate when it was published, but can change without notice. Please be sure to confirm all rates and details directly with the companies in question before planning your trip.