Wat Ounalom is the most significant pagoda in Phnom Penh. Located close to the riverside, it is easy to get to and can be accompanied by a visit to the Royal Palace. Dating back to 1443, it consists of 44 structures. It was damaged during the Khmer Rouge but has since been restored. I particularly enjoyed visiting the stupas and statues around the back.
Entry is free, though you may want to bring some small riel to make an offering.