I don't generally read Year That Never Was fics -- there aren't many of them written, and those that exist are often about Jack witnessing the slow, painful deaths of his team.

The one I do have in my bookmarks currently is a Iantocentric story called Paradox (http://tbb.destinysgarden.net/submissions/22_paradox.html), about Ianto escaping the Toclafane and hiding out in the deep heart of the Hub. I -- am not sure that I liked it, and I found the ending deeply disappointing, but I also found points in it very interesting and the idea is quite captivating. Plus there's some lovely worldbuilding with the Hub.