After struggeling with Endnote (4), I searched for other applications. I found Mendeley on the WWW. It is very easy to work with and perhaps an idea to look at. Today (09/02/2012) I have received a newer version of Endnote (5) and it looks like the Mendeley version I am using. Decide for yourself what fits you the best.
http://www.mendeley.com/ for more info.