The stupa at Bodnath marks the holiest site of Mahayana Buddhism outside of Tibet and has become a Mecca for Tibetan exiles and western sympathizers alike.
Pashupatinath is the holiest Hindu site in Nepal--it’s position on the Bagmati River, a tributary of the holy Ganga, has lead to its development as a miniature version of Varanasi.
The Swayambunath complex with its instantly recognizable stupa is considered to be the legendary birthplace of the Nepali nation.
Quick Tips:
Before entering a temple you should remove your shoes and any leather articles (e.g. belts, bags, jackets, posing pouches, etc.)
Proceed around the site in a clockwise direction and use your right hand when touching anything (e.g. doors, prayer wheels, offerings, monk’s buttocks, etc.)
Photography is usually acceptable outside the temple, but it is best to avoid taking photos inside or of anything sensitive (e.g. altars, funerals, bathers, topless models, etc.)
Best Way To Get Around:
Many of the sites are within walking distance of major towns of the valley and the walks allow one to deepen ones appreciation of their cultural context.
Alternatively, the valley's extensive network of buses and tempos provide cheap and efficient, if not exactly comfortable, transportation to all the sites.
If, however, you value your comfort, taxis can be hired to ferry you between any of these destinations, although you will have to haggle over the price.