You also need to look at what is being done with the VISTA project at Lawrence Berkeley Labs. The goal of VISTA is to identify distant-acting transcriptional enhancers in the human genome by coupling the identification of evolutionary conserved noncoding sequences with a moderate throughput mouse transgenesis enhancer assay.
Be sure to also explore the ENCODE data, in the regulation section, for several TFBS data sets that have new and interesting stuff. It is found in the UCSC Genome Browser, mostly on the human Mar 2006 assembly right now. I just saw the first mouse stuff come in, but it's pretty limited right now.
I second the VISTA suggestion as well. Their Enhancer Browser is a very neat project.
i suggest you try Genomatix, it is very interesting database and also tools for promoter analysis. you can retrive promoter region, too. but at first you have to register by a academic email after that you can use it free for one week. i really suggest you see this site.