There are two answers to this, depending on what time you're talking about.
Daytime: Walking. Phnom Penh is a great city for walking, with everything really within the enthusiastic walker's reach. Lakeside to Wat Phnom takes about 30-45 minutes at a reasonable pace. Though motos are cheap and persistent, try to spend at least some time walking. If you'd had your fill, motos are fast and cheap and cyclos are slow and cheap. To be safe, you can try to negotiate a fare before jumping on, but often drivers won't speak enough English, and confusion can arise between "one" meaning 1,000 riel or $1. We find it's generally fine just to jump on and pay when you arrive. Sample fares for motos are (roughly) lakeside to Wat Phnom 1,000-1,500 riel, FCC to Tuol Sleng 2,000 riel, Russian Market to lakeside 2,000-3,000 riel. Prices usually rise up to double after dark. If you offer payment to the moto and he refuses to take the money, then you have definitely not offered enough, so up it. You are not expected to pay in dollars, though they are accepted. If you try to pay with anything bigger than a $1 note, don't expect the moto to have change. If you plan on tripping around a lot, you can hire a moto for the day, figure around $5-$8 a day depending on where you are going and how well you negotiate.
Nighttime: Walking from one end of town to the other at night is not a good idea. Theft and assault remain problems in Phnom Penh -- walking long distances at night dramatically increases the risk of a problem. Walking from Sisowath Quay to lakeside around midnight after a happy pizza and beers is plain stupid. Use motos or cyclos for anything more than a few blocks.
Please find below some of the more frequently asked questions (FAQ) people have about travelling to Cambodia. We've tried to answer all the most frequently asked questions, but if you have another query about Cambodia, please try our Travelfish messageboard.
Is a fan room okay, or should I budget for air-con?
Is it possible to rent rooms or dormitories for longer periods of time while travelling in Cambodia?
Should I take my own padlock for the door of my room while travelling in Cambodia?
What should I do if a bag is stolen from my room or dormitory while travelling in Cambodia?
What standard of accommodation can I expect for US$5 in Cambodia?
Why are there so few dormitories in Cambodia?
Why are there so few hostels in Cambodia?
Can I drink the tap water in Cambodia?
How can I avoid MSG in Cambodia?
How do I avoid peanuts in Cambodia?
I have a food allergy -- what should I do when travelling in Cambodia?
Is there good vegetarian food in Cambodia?
Is western food available in Cambodia?
Are the ferries in Cambodia safe?
Are the trains in Cambodia safe?
Do the trains run on time?
Is it easy to hitch-hike in Cambodia?
Is it easy to rent a car or motorcycle in Cambodia?
Should I get a tourist minibus in Cambodia?
What's the best way to travel around Cambodia -- share-taxi, bus, train or boat?
Are credit cards accepted in Cambodia?
Are there ATMs in Cambodia?
How can I have money sent to me in Cambodia?
How can I send money out of Cambodia?
Should I bring travellers cheques, credit/debit cards or cash to Cambodia?
Should I tip in Cambodia?
Are leeches a problem in Cambodia?
Are legal drugs cheap in Cambodia?
Do I need a prescription in Cambodia?
Do I need malarial medication in Cambodia?
HIV/AIDS in Cambodia
Is heatstroke a problem?
Is medical care cheap in Cambodia?
Is medical care in Cambodia good?
Is rabies a problem in Thailand?
What about dengue haemorrhagic fever in Cambodia?
What about schistosomiasis in Cambodia?
What general food and water precautions should be followed in Cambodia?
What general health advice can you offer for Cambodia?
What should be in a traveller's medical kit for travel in Cambodia?
Will I get diarrhoea in Cambodia?