After three days in Istanbul, we began our travels around the country by taking a bus to visit the site of ancient Troy. Coincidentally, we wound up using the Truva ("Troy") bus line whose corporate symbol is the Trojan Horse.
Buses are the means of transportation of choice for long-distance travel in Turkey. Planes are rare and pricey, trains are cheap but there are few, but buses are plentiful, comfortable, and cheap, with stewards serving hot tea, a refreshing spritz of cologne, and sometimes snacks. Some buses are more comfortable than others, however. Once Paul got stuck in a seat in which he could feel the tray table of the passenger behind him in his back; and once we got suckered into taking a small non-air-conditioned bus by a tout at an bus station (autogar); but mostly they were fine.
Expect reserved seats (sometimes not as strictly enforced as others--if your seat is really bad, try asking the attendant if you can move. Although buses to most locations are frequent, you probably won't know in which locations it's important to make an advance reservation. The best plan is to go shopping for a reservation for your eventual departure when you first arrive at the autogar, but it's hard to resist the momentum to get you off to your hotel and postpone bus tickets till later. You may well find yourself miles from the autogar when you're preparing to leave, and then it's often worthwhile to work through a travel agency. They they charge a premium, but usually use superior bus companies and provide a shuttle to take you from your hotel or their nearest office to the autogar. Buses are so cheap in American dollars that this service makes a lot of sense.