Chmoogle accommodates automation
"You may perform an unlimited number of searches on Chmoogle from a standard web browser application which is under your immediate personal control. If you use an automated system such as a script or program to search Chmoogle, you may only access the first one hundred pages (1000 compounds) for each distinct query, and you may not access more than one thousand pages (10000 compounds) in any twenty-four hour period."
This is very nice. Note, however, that they do not make an API available.
Also they will be incorporating the Sigma-Aldrich catalogue in a few weeks - that will take Chmoogle to a new level of usefulness for automated queries.