For me, Boxee is all about watching TV shows and movies I download from the Internet or rip from my DVDs. This means I spend most of my time in the "Video" section of Boxee.
I really like the ability to change view-types and sort order.
Since this area lists all the indexed content, I'd like to see better ways to group and manage the content. There's already a logical grouping for "Internet video". I'd like to have the ability to group for genre or type (movie, TV, video podcast).
I think the "My Sources" could be moved to the navigation bar with menu and options. A search option on here would be great too.