wickedboston - 9:45 pm on Apr 5, 2011 (gmt 0)
Some queries certainly have different results which do not appear to be solely due to a laten server update - however I do not believe results are different because of penalties. I could not find any results for the companies which were recently publicly penalized - could you?
One thing I noticed that was interesting was that the CSE results show multiple listings for the same domain but in Google they only showed one result - indent listings are definitely being used less. It is also interesting to note that Google put the internal page in their results over the homepage, even-though the homepage was ranked higher in CSE. The internal page was moved to the position of the homepage and the homepage was completely removed from the results.
Try a search for 'dresses' almost all the results are homepages in CSE but not in Google..