The two sites have very different layout when you first get to the home page. They both display the most popular videos on the home and give you the ability to search for things at the top. However, Hulu has other catagories such as: recent videos and my videos. There is also an section at the top with advertisments for movies that are are about to be released in theaters. Youtube, on the homepage, doesn't appear to have an advertising at all.
Overall, the two differ the most in quality and the diveristy of content. Youtube has more to offer but a lot of their videos aren't the best quality. Hulu on the other hand has a better selection of TV shows even though it does not give you the ability to post your own videos or view music videos.