There are several sites designed to help you find the perfect hotel. This experiment from Google leverages some of the search giant's strengths, with a map-based and search filtering approach.
To narrow down where you want to stay, you can draw shapes on the Google map, defining one or more neighborhoods. The resulting hotels list can be sorted by hotel class, user rating, price — and, very interestingly, price for your travel dates compared to the typical price over the last year (so you can see if it's more expensive to stay at that hotel now that it normally is). You can also add hotels to a shortlist for easy comparison later.
It's still an experiment and only in the US right now, but promising nonetheless.