The major bus company on Crete is KTEL....
KTEL is the national bus company of Greece and has services almost everywhere anyone might ever want to go.  I can get from my local bus stop in Kolimbari to almost everywhere else in Greece at amazingly good prices within a day.  Although from Kolimbari my day will have to start about in the early evening, changing at Chania because the bus to Athens will have to catch the ferry to Piraeus (Athens seaport).  Not many holiday-makers might want to go that far, certainly not on a short holiday. 
But certainly you can tour Crete by bus staying overnight in different places in the certain knowledge that your transport will be there next day.  Any KTEL office will supply tickets; book seats and supply schedules.  Be aware though that although the majority of the main-route buses are in fact Pullman coaches, complete with air-conditioning; comfortable seats and all mod-cons, some, particularly those traveling to the remoter destinations, may not be!  It is best to book a seat if your journey is long or you need to sit, but don't be surprised to find your seat occupied or afraid to reclaim it.  Locals will not know the seat is booked unless you tell them.  Or ask the conductor to assist.  Remember that the conductors will load your luggage if you have some and return it at your destination.

On major routes in and between tourist areas in season the crews are happy to deal with foreign visitors and usually make sure you don't miss your stop.  But beware, although bus inspectors are both helpful and frequent, they will want to see your ticket...  Or ask you to pay if you can't produce it!

Go by Bus  - 'Me to leoforio' ..
Wait in the shade at the main KTEL bus station in Chania - next to the Omalos Hotel.  Main route buses on Crete are green and cream coloured.  Regardless of what the destination a bus shows - check the number in the top centre of the windscreen.  If in doubt ask the driver or conductor!!
In town the system is different...
The local buses run only within the city limits, although this means some kilometers outside.  In Chania they start from outside the market hall and opposite next to the National Bank of Greece.  Buy your tickets from the small kiosk next to both or from a Periptero near a stop.  You MUST cancel your ticket by giving it to the driver - who will tear it in half and give you a half back!


To add to the confusion both types of bus appear to stop sometimes at the same places.  If you are in any way uncertain ask the driver when you climb aboard.  Catch them at bus stops.  If you are uncertain of their whereabouts ask when you buy your ticket.  We were saved a long walk from the outskirts of Athens recently when we waved down a local bus away from a stop.  They don't have to stop but this one did.  A piece of luck as it was carrying an inspector who was able to sell us tickets, otherwise we would have been footsore and well cooked before finding the next stop to swelter at.  And mobile 'phones don't always save the day - ours, on that occasion, didn't.