Quick post just to direct your attention to two recent interesting papers using ChIP-Seq [See also [Techniques] Analyzing the genome-wide chromatin landscape: ChIP-Seq].
Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq. Bioinformatics. 2010 Mar 5. [Epub ahead of print]
Annotation of gene promoters by integrative data-mining of ChIP-seq Pol-II enrichment data. BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S65.