I generally dislike any yaoi and yuri stories, no matter who's in it, so somebody else will need to answer Amaranth's question.
Personally, I like stories that are unique and different. Story ideas that are really overused I do not like, like the whole Ran finding out who Shinichi is thing. If you can change up the concept so it looks different, then I'll like it, like my The Fake Caller story, or my Gin's Future story. One deals with Ran finding out about Conan, and one deals with the defeat of the BO, though those aren't the main focus. Stories with an interesting premise I'll generally read. As to what to recommend, I think the best ones have already been put up, unless you count mine, which I consider OK but not great.
http://www.fanfiction.net/u/3088688/CoolKid94