Taking public transport in Nepal is a once in a lifetime experience, and you'll have a lot of history to tell when you get home.
In cities, the best way to get around is by rickshaw. If you prefer to take a taxi, make sure the taxi is licensed with the taxi sign on the roof and a black number plate. You can also rent vehicles. There are more comfortable but more expensive private taxis.
Around the Katmandu Valley, public government buses are green. They will only stop at official bus stops.