Unless there was a written work-for-hire contract, it's going to come down to the exact nature of the relationship between Dawkin's foundation and Timonen. There is some mention of Timonen working through his own company, in which case he was not legally an employee of the foundation. If the works in question were produced under that arrangement, then without a written work-for-hire agreement the works belong to Timonen.
I myself have run into work-for-hire disputes before. Unless you're an employee or you otherwise agree in writing to relinquish ownership of works you produce, they're yours.
http://www.copyright.gov/circs/circ09.pdf
According their 2008 and 2009 Form 990 filings, Timonen was not an employee at all. He was a contractor. He claimed rights to the DVDs, but contributions to audio-visual productions are specifically exempted as being considered work-for-hire, so his claim there is wrong. As for the website and the logo, if there's no work-for-hire contract, there can still be the issue of joint copyright if they worked cooperatively. If the foundation wrote the blurbs for the DVDs (like if they were taken directly from the DVD cover or included quotes from the DVD itself), the copyright will most likely belong to them, and that will be resolved with the effort put into making it into a web page.