My favourites would have to be...
Sci-fi
Homecoming by Louise. It's only a few chapters in, but I'm completely hooked. It begins at the end of a war with an enemy planet and all the boys are in it.
Chronos Project by Lore. Again, only a few chapters written by loving it so far. A woman is transported through time and every so often, she jumps to another time, but can't seem to find her way home.
Whatever The Night May Bring by Mare. Really love this one too. All the boys are in it and it starts off with them crash landing whilst on their way to do some promo. The place they land in is not what they are expecting!
Fantasy
Brian Potter & The Malevolent Musician. It's a BSB and Harry Potter crossover and very good.
On Nightingale Hill. This story is just amazing and I wish it would be updated more often than it is. Nick ends up in this strange land where he's the only person, until he meets a magical little girl who grows at an unusual rate.
Only In My Dreams. This is a romance/fantasy where Brian falls asleep and the things he dreams about become reality. Very entertaining story.