One of the typical distinguishing characteristics of Santa Fe accommodations, as you might guess, is the use of Spanish Colonial and Pueblo Revival architectural elements - latilla-and-viga ceilings (a style in which smaller wood poles are laid crosswise upon larger wood beams), kiva (beehave-shape) ovens, Navajo and other Indian rugs and textiles, and built-in bancos (benches) and similar shelves and features. You'll find these especially in B&Bs set inside historic adobe houses, but also - to an extent - in larger hotels.
Here's a list of the properties included in this article (in alphabetical order). Scroll down and click on the link to go to that property description directly. If visiting the Duke City, also check out the Albuquerque Guide to Gay-Friendly Hotels and B&Bs.
Buffalo Thunder Resort & Casino
Don Gaspar Inn
El Farolito Inn
El Rey Inn
Four Seasons Resort Santa Fe
Hacienda Nicholas/Madeleine Inn/Alexander's Inn
Hotel Chimayo de Santa Fe
Hotel St. Francis
Inn of the Anasazi
Inn of the Five Graces
Inn of the Governors
Inn on the Alameda
La Posada de Santa Fe Resort
Santa Fe Sage Inn
Ten Thousand Waves
Triangle Inn Santa Fe
The GLBT travel market is a prominent one in Santa Fe, and several inns are also owned or staffed by local gay and lesbian residents. The properties I've written about here are mostly independent and rather distinctive, but Santa Fe does have a large variety of chain motels and hotels, mostly set along busy and not particularly attractive Cerrillos Road, a few miles southwest of downtown, which is anchored by the historic Plaza and where you'll find most of the city's notable attractions, restaurants, and retail.
The Cerrillos properties are fine if you want a good value and have a car. But if you're seeking a property with more character, check out some of the ones I've included here, the majority of which are within walking distance of the Plaza. On that note, if you do stay in the center of the action, you can easily get by in Santa Fe without a car. But, given that the entire north-central New Mexico corridor offers a wealth of things to see and do and dozens of spectacularly scenic drives, you may want to rent a car anyway, if even just for a day or two of exploring (there are some rental agencies in town).
Santa Fe has a small airport with regular service on American from Dallas and Los Angeles. Most visitors fly into the much larger Albuquerque International Sunport, which is just a little over an hour away and also has regular shuttle bus and train service into town.
A note about B&Bs: if you're not typically a fan of guesthouses and B&Bs because you prefer a bit more privacy and insulation from fellow guests and innkeepers, you might give Santa Fe a try anyway. At many smaller properties here, accommodations are in detached or semi-detached casitas (cottages) with separate outdoor entrances. And even when breakfast is included, guests at many properties have the option of dining in-room or at least at a private table. Guesthouse rooms are often significantly larger than hotel rooms, and they sometimes have private gardens or patio, small kitchens, fireplaces, and other appealing features. You may want to read a bit more about some of these, visiting their websites as well, before deciding.