I travel quite a bit and use several of the hotel sites. I generally narrow the choice of hotel down to two or three and then check 3 or 4 of the sites comparing prices. If I am travelling in a few months time I wait until one of them has one of their "sales" before booking. For example Aer Lingus had a 10% sale recently on the launch of their aerlingushotels.com site. I compared prices to make sure that it was a genuine 10% sale, which it was, then booked through them. However next time it might be a different site that I use.
www.octopustravel.com
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http://www.venere.com (www.venere.com)
Some sites have better maps than others and some sites offer hotel reviews that can be very useful. Don't stick with one site is the advice that I would give.