If you're going to the Gallipoli peninsula from Canakkale, then you have two ferry options: one that arrives in Eceabat and other that arrives at Kilitbahir where the old fortress is located.
The Canakkale-Eceabat ferry runs every hour on the hour from 7am-1am and then 3am & 5pm (with sailings every 30 minutes during the busy summer period). I took my hire car across and it cost TL23.
The Canakkale-Kilitbahir ferry runs at 7am, 8am, 8.30am, 9.15am (and at 15 mins past the hour until 6.15pm), then 6.45pm, and then every hour on the hour between 7pm & midnight. There are also extra sailings in the summer at 45 mins past every hour between 9.45am and 5.45pm.
Çanakkale Province has territory in both Europe and Asia. Ferries cross here to the northern (European) side of the strait. Regularly scheduled ferry boats make the trip from Canakkale to Eceabat for a 25 minute journey across the Dardanelles.
There are also ferryboats running between Çanakkale-Eceabat, Çanakkale-Kilitbair, Gelibolu-Lapseki, Bozcaada-Odunluk, Çanakkale-Gökçeada and Kabatepe-Gökçeada.
You can watch my 2 min 04 sec HQ Video Canakkale slide show Part II out of my Youtube channel with Turkish pop music by Goksel – Gunun Brinde.
You may watch my high resolution photo of Çanakkale on the Google Earth according to the following coordinates 40° 9' 3.50" N 26° 24' 8.99" E or on my Google Earth Panoramio Çanakkale Ferryboat .
We reached Çanakkale by our excursion bus from Troy on our way to Istanbul along E87 (about 30 km). We crossed the Dardanelles from Çanakkale to Eceabat (about 6 km) and reached Europe from Asia!
Transport from Çanakkale to Troy, Assos, Alexandreia -Troas and other centres are very easy. There are regular buses running to important centres such as Troy and Assos from the centre of the city.
There are no bridges across the Dardanelles. In order to get from the European side to the Asian side, you must take a ferry boat, which runs regularly between Eceabat on the European side and Canakkale on the Asian side, carrying cars and trucks as well as passengers. The boat ride took about 30 minutes, but you need to get there a little early if you are driving, in order get in line. Once you park your car on the ferry, you can get out and walk up to the lounge where they serve snacks and drinks.
Make your way to the otogar (bus station) in Istanbul. (Take the tram from Sultanahmet to Aksaray or Yusufpasa, then the metro train from Aksaray metro station to Otogar 1.40YTL per mode of transport). There are probably about 5 different bus companies that serve Canakkale. Truva Turizm (coach of the year 2008) have hourly buses at all hours, weekdays and weekends, to Canakkale. 40YTL, 6 hours, just over 300 kms with many stops along the way. Other bus companies are Metro and Kamil Koc. The coach will go south down the europe side of Turkey, before boarding one of the frequent ferries at Eczeabat, for the 30 minute journey to Canakkale on the Asia side of Turkey. In Canakkale, the bus stops just after it leaves the ferry. The bus offices where you can purchase a ticket to Istanbul or south to Izmir are right at the ferry docks.
In Istanbul city centre, you can also pre book your coach ticket from any tourist agency. They charge the same amount of 40 YTL. You still need to make your own way to the otogar, however some companies do offer pick up from the Sultanahmet area.
If you want to cross to Canakkale from Eceabat or reverse, there is a convenient ferry. Tickets are purchased outside the ferry entrance, on the right as you drive in. Be there 30 minutes before departure time if you're driving, 15 minutes before if you're on foot. Tickets cost about $5 per car, $2 for a bike and $1 per person. I don't know if these prices have changed.
Vendors are there to sell you meat, clean your window and so on. The trip across the Dardanelles takes about a half hour, and you can get out of your car and wander around.
Ferries from Caakkale to Eceabat leav at 2 and 4am, then hourly from 7am to midnight. During the summer, they sail every half hour between 7am and midnight also.
From Canakkale to Eceabat, ferries leave at 1, 3 and 5 am, then hourly from 7am to midnight. They also depart every half hour in the summer from 7am to midnight.
There are other ferries out of Canakkale, such as the ferry to Kilitbahir, for which you go to the Kilitbahir dock or supposedly there's a small dock near the Hotel Bakir. I don't know about prices, but it may take 15-20 minutes.
There is also another ferry between Gelibolu and Lapseki (both cities are northeast of Canakkale and Eceabat. There are more ferries in the morning, it seems... From Lapseki, 2 and 4am, 5:45, 6:30, 7:30, 8:15, 9:00am, every hour on the hour after that until midnight, summers every half hour between 7am and midnight. From Gelibolu, 1, 3 and 5am, 6:30, 7:30 and 8:15am, then every hour on the hour until midnight, every half hour in the summer.