There are many different groups that are developing software for finding transciption factor binding sites, alongside our own development of the BIFA tool which forms part of the Apples framework

Toucan/Toucan2

Available from:

http://homes.esat.kuleuven.be/~saerts/software/toucan.php

A Java application that reuires a local installation of a database that provides binding site information (eg the Public Transfac 6.0 data).