There are many very good hotels in all price bracket in Kathmandu this isn't meant to be a list of all options but just some ideas to get you started.
On the budget end, I like the area of Paknajol which is near the northern end of Thamel but not in Thamel (the main tourist area in Kathmandu with lots of restaurants, hotels, and shops catering to tourists). Most guesthouses there have gardens and are much quieter than Thamel. This is the area I used to stay in when I first started coming to Nepal. Some of the hotels include: Nirvana Peace Home, Kathmandu Garden House, Yellow House, and Kathmandu Peace Guest House.
In the mid-range people seem to like Hotel Ganesh Himal, though I haven't personally been there.
The Yak and Yeti and Sharkar Hotel are popular hotels on the higher end and are close to Thamel (a 10 minute walk or so). Kathmandu Guest House, another popular high-end hotel, is in the center of Thamel.