Some hotels want to cater for gay clientele. Over the past years, the number of gay hotels has gone down considerably. Being gay is just not an issue any more in any hotel (but see the rise of MisterBnB below).
The gay hotels that we know are listed here.

Hostelle is listed here, as it is the only women-only hotel in Amsterdam. It is not specifically a hotel for lesbian women.

A new development (in 2015) is Misterbnb (has nothing to do with leatershop Mister B). Apparently, there is demand for gay-specific accommodation, according to MisterBnB. It lists private rentals, ranging from cheap rooms, to large apartments and houseboats. The site specifically targets a gay audience, and works just like AirBnb. It might run into the same problems with the authorities, regarding tax laws, safety regulations and illegal hotels.