Boxes is a media center application based on XBMC for coralling all your media (movies, music, video, etc) into one place. Boxee has a much stronger net video focus than XBMC (at the moment, at least) and provides simple access to Hulu, CBS, ABC, YouTube, and others.
I just revised my media setup and evaluated all the options available but decided against Boxee. I chose Plex, which is another Mac-centric branch of XBMC, along with MythTV for TV recording. I found the net video content on Boxes to be pretty lame (IMHO). It’s mostly really old TV shows and lame movies. I also really hate how all the content is divided up into fake “channels” like Hulu, ABC, etc.
On the other side, Plex doesn’t have all the net video options of Boxee, but it does have excellent iLife integration so that from my TV, I can access all my iPhoto and iTunes libraries from my other computers around the house, as well as videos and recordings from my Linux media server.