Here is my experience the one and only time I used an online discounter. Over the course of a year, I had stayed twice in the same NYC Hotel which I had booked through their web site. It was a tourist class hotel but both stays I found the rooms to be quite spacious, clean, modern and overall very good.
My third stay I went with hotels.com and got a better rate then I had gotten by booking directly with the hotel previously. I was very pleased to be staying at an establishment that was known to me and at a good price. However, the room we were assigned upon check-in was so unsatisfactory I found it hard to believe that it was part of the same hotel. It was tiny, (you literally had to edge past the bed to get to the dresser), dark (no natural light), stunk of smoke (although it was non-smoking) and had a view of the back of a building (which explained the lack of light). I quickly returned to the front desk to request another room. Reluctantly the front desk assigned a marginally better one. I realized then that I was most likely given the worst rooms in the hotel because of the price I was paying. Which, basically I understand is only fair. Why should those who are paying close to rack rate get the worst rooms?
Now whenever I book it is only through a hotel's web site so I don't have a repeat of that experience. But I have friends that use priceline all the time because they aren't as picky as I am. Sometimes they get dumpy rooms, sometimes they get great ones.