I've embedded the links in the story titles or in the part number, so just click on those and you should go straight to the fic.
First up have to be my favourites from
Miles To Go Before We Sleep [PG-13] (1 Part) and
Promises To Keep [PG-13] - Part 1 Part 2
Next comes Forever For You - An Alternate Tale Of The 456 by veronicaluv - this one is adult rated, so beware. The link is to the full story in one piece rather than in chapters.
Then there's When Everything Changed [PG] (20 Parts) by tonjavmoore - the link is to the first part, there are links at the end of each chapter to take you to the next part.
Finally, Lazarus [Mostly PG] (31 Parts) by ladyreapermc - again, the link is to the first part and each chapter links to the next.
Hope you enjoy. If I get any more suggestions, I'll add them to the post.
Here are a few more suggested by my lovely friends!
Throughout Time And Space [NC-17] (25 Parts) by bassair
Chosen [PG-13] by blackhemlock
The Rose Of Jericho [M] (5 Chapters) by kaydeefalls - Link is to Chapter 1
Once Lost [M] (6 Chapters) by Jax25
The Jacks [T] (30 Chapters) by Tylluan
Do Not Stand At My Grave And Weep [M] (5 Chapters) by black.k.kat
Promises [M] by Gryvon
The Archivist [U] by adina_atl
Get Your Bearings [NC-17] by marita_c
How Ianto Jones Saved The Future [A] by Chocolatephysicist
Ghost Story [T+] by mad_maudlin