Well, B-Sides are becoming a thing of a past. Actually, they are morphing to what 'Samba Nova' is, an extra track.
Pearl Jam is well known for B-Sides. Their newest album, Backspacer, has no actual B-Sides. All of those tracks are replaced by other songs from the album. I guess this isn't the best example to use since they did not have a Deluxe/Special edition of the album.
At this point, I prefer extra songs on the deluxe version of the album as opposed to placed a B-Side. Yeah, its not the same, but it is one less thing to buy - plus it helps organizing songs on my iPod more efficiently.
Samba Nova is a great track regardless. I am happy to have it wherever it falls on the album.