In order to be an effective "social" media player, where titles can be shared and recognized by others, it has restrictions on the media sources. If your content isn't in IMDB, Hulu, TV Guide, or one of the other supported providers, there's no way to get it into Boxee.
The biggest offenders are TV series on DVD. Boxee understands Battlestar Galactica Season 1, Episode 5, but can't parse the DVD rip of Battlestar Galactica Season 1, Disk 2. Or, likewise, the DVD rip of Pixar's Short Films Collection (but it can parse the individual short films).
To be fair, last time I checked, none of the XBMC forks could parse these media (someone really should write a Netflix scraper plugin), but at least you could manually enter them.