Here is travel advice to help you enjoy your stay in Nepal.
The most important thing about Nepal is to have fun and be prepared for culture shock. Being a foreigner, you will be hounded by locals to buy stuff and will pay more, often much more, for everything. Remember that even though you are paying more, it is still usually less than you would pay for the same thing at home. That is part of the trip. Accept it and have fun. You can haggle if you wish. Too many people stress about paying more and do not enjoy anything. Accept it as a fact of travel and another expense so you can enjoy it. You can familiarize yourself with prices before going if you want an idea of what locals pay.
When you arrive at Customs in Nepal you will have to pay for the Visa in USD or equivalent.
Do not drink the water. Ever. Even if the locals drink it. Even if your are told it is filtered and boiled. Our bodies react violently to pathogens they have adapted to. Only drink water after using chlorine drops, drink bottled water, or sanitize and purify it another way. You can buy chlorine drops for at least 50 liters for less than one USD at a local pharmacy. If you use bottled water check to ensure it is in a clean and sealed bottle in new condition. Crush the bottles when you are done so that it is clear they are used.
If you are flying, always be near the airport a day or two early. Traffic, protests, or any number of issues may delay you.
You can fly to the main areas if short on time. You will pay much more than locals and there is no way around it. There are comfortable tourist buses to allow you to enjoy the scenery. Look up the bus company beforehand. Use a higher end bus for increased safety. A good bus company that goes to the main tourist sites is Greenline. They are air conditioned, drive less erratically, and seem safer. I used a different company that said they have air conditioning, but it was only a bottle of semi-cold liquid that ran out quickly into the trip. We then had to open the windows to dust, dirt, noise, heat, and started sweating. Use Greenline if you want a more comfortable journey.
All transportation is notoriously unsafe. I used local transportation to save money like: Tuk Tuk's, minibuses, vans, and normal buses. It can take more time, they will be packed, stop for anything, be dusty, smell, and are not climate controlled. But it can be part of the experience.
In Kathmandu three top things were seeing the Swayambhu Temple (Monkey Temple) for a nice overview of the city, the Royal Palace, and Dharahara for another view of the city. Foreigners can cut to the front of the line at the Royal Palace. Talk to an employee if need be.
For Pokhara, Annapurna, and Everest, it is unnecessary to book lodging in advance because there are plenty of places to stay.
Pokhara is a top destination. Many people trek in the Annapurna region for a couple weeks. You will not see Mt. Everest from there. Pokhara has a lake and cave with a stream / river running through it. Walk from the bus stop. Lodging is nearby. Simply walk along and pick somewhere to stay from the numerous places along the water. Touts will hound you to come with them. The easiest thing to do is confidently walk past them. You can ask them to point you in the direction of the waterfront.
I went to the Everest region. Tengboche is a really nice place to visit. It has a wonderful view of Everest and a nice temple. The atmosphere is amazing. I took a flight from Kathmandu to Lukla and started hiking from there. You do not need a guide. Keep an eye on altitude sickness, consider medication for it beforehand, and take your time. I became altitude sick and later found out that people die from it. Spend a couple nights in Namche Bazar to adjust to the altitude and hike up only ~300 meters (~1000 feet) in altitude per day after that. Rest a couple nights every ~1000 meters (~3000 feet) to adapt to the altitude. There are plenty of places to stay on the way when you are tired. You do not need sleeping bags or bedding. Bring only what you need. Everything feels heavy after eight hours of hiking in a day. Some places offer to store things for you in Kathmandu if you have extra stuff. Meals are generally 300 rupees (~3.50 USD) each and lodging another 300 rupees per night (as of 2010). Bring enough money for the whole trip. There are no ATM's. A solar charger for your camera will be useful. Or you can pay ~300 rupees per charge or hour (depending on the place) on the way. You can buy chlorine drops from local pharmacies in Kathmandu to sanitize the water for really cheap, buy bottled water for about 100 rupees per liter, or use another option you may prefer. I used stream water and added chlorine drops and was fine the whole time. There are plenty of places to eat and sleep in the area. You do not need a guide as there is only one way to go. The trail splits at one section, one going to Gokyo Ri for a nice view of Everest, and the other going to Tengboche and base camp. There are signs along the way announcing the split. Stay on the trails. If you want to go to Gokyo Ri and base camp, allow about three weeks to do it comfortably. Or a week and a half to two weeks if you will only go to one of them.
Lumbini is the purported birthplace of Buddha. It was a nice stop. If it is summertime it will be very hot! There are ruins of old buildings and enough to check out for the day, maybe more if you're into that kind of stuff.
Visit the Nepal Wikitravel page for additional useful information.
Visit my Nepal page for my personal experience there.