Central Çanakkale is small enough to walk: the ferry pier, Cumhuriyet Meydanı, the Trojan Horse, and Çimenlik Castle are all within ten minutes of each other along the waterfront.
To Gallipoli — the easiest option is the car ferry across the strait to Eceabat (around 25 minutes, frequent), which puts you on the European shore where the battlefields are. Tours from Çanakkale and Eceabat include the crossing.
To Troy — local dolmuş minibuses to Tevfikiye (the village beside the site) leave from the bus station behind the main square; the journey takes around 45 minutes. Returning, the last dolmuş back is in the early evening.
Within the city — taxis are cheap, plentiful, and metered. The main bus station for long-distance services is a short taxi ride east of the centre.