At least when talking about prog rock it seems like most people call songs "filler" when they're experimental and/or very different.
So in that case I'd say that "filler is experimental songs/segments that the band really digs and decided to include on the album, even though they realize it's different and might not appeal to most listeners". I like that kind of "filler" though, since they show more of the song-writer's personal preferences.
