Crete is Greece's largest island. While it has charming villages galore, Crete has something that no other Greek island can claim - a city. What's more, Crete has five of them, all adorning the north coast.
Crete's multiple metropolis should come as no surprise - even in very remote times, Crete was known as an island of cities, ninety of them, according to Homer. While these ancient sites were hardly "cities" in the more modern sense, they were centers of trade, industry, government, and defense. What's more, the modern cities of Crete seem to have appeared on top of the ancient ones, giving us the idea that the Minoans would have few problems with modern city planning. They chose good locations three or four thousand years ago, and we haven't improved much on their choices.
Heraklion - Capital of Crete
Once called Candia or Kandia, the city of Heracles or Hercules occupies the site of an ancient Minoan port. The Minoan palace site of Knossos is a short distance inland, on the side of what was a navigable river in ancient times. Knossos itself is built over a Neolithic site which may be the earliest permanently inhabited site on Crete, making it - and Heraklion - among the oldest inhabited sites still in existence today.
More on Heraklion:
Chania - The City of the West
Chania, also called Hania, Xania, and similar variants are located in the west of Crete and is adjacent to the large town of Kissamos. Chania has been an important port throughout its history, and probably retains a memory of Minoan seafaring - roads were not as crucial as waterways, so regularly-spaced, large ports were probably a feature of ancient Minoan life as well. Chania has a busy airport and is also adjacent to the American base at Souda Bay, attracting many U.S. visitors.
Located between Chania and Heraklion, this port city is not as well known as its neighbors to the east and west. It has a charming historic district and because it is less popular, the prices are lower on hotels, restaurants, and even souvenir shopping.
Home to an excellent Archaeological Museum which showcases the mysterious large ivory figurine called the Palaikastro Kouros, Sitia has a small port providing access to some of the Dodecanese islands and beyond. A small airport is under consideration for expansion, so Sitia may soon be a viable alternative to arriving in Heraklion.
The easternmost city of Crete, Agios Nikolaos is near to the luxury resorts of Elounda and the ancient town of Lato, and it also is a stop for some ships to the Dodecanese islands. It has an excellent Archaeological Museum, a deep inner bay alleged to be bottomless, and numerous restaurants and nightclubs.
Mallia or Malia
While Mallia doesn't quite qualify as a city - it's mainly a row of restaurants and bars, with a few shops and little if any local industry other than serving tourists beverages - it too is built on a site originally chosen by the Minoans, who erected the well-curated palace of Mallia along the coast.
Mires and Tymbaki
Larger towns in southern Crete at the seaside edge of the Mesara plain, these towns are agricultural hubs with relatively few hotels or other accommodations. That's left to the smaller towns in the region, including the pleasant village of Kamilari, the seaside resort town of Kalamaki, and the famed "Hippie Town" of Matala. If you travel by bus from Heraklion to visit the ancient Minoan palace of Phaistos, you'll usually change buses in Mires. Mires is also spelled "Moires", in particular on signs marking the road from Heraklion, so if you're driving, look for the alternate spelling. It hosts a street market on Saturdays and boasts a couple of car dealerships just outside town. Both towns depend on local trade rather than tourist purchases.
Other important towns on the south coast can't quite be called cities, either, but include Paleochora to the west, Chora Sfakia on the coast, and Ierapetra to the east. Chora Sfakia is the capital of the Sfakia region, but still, maintains a seaside village feeling and can be reached by both road and ferry. It's a stop for many tourists visiting the Samaria Gorge, as the ferry deposits thousands of them each day to board buses back to the north coast of Crete after descending through the Gorge.