Well, there is When Pandora's Box is Opened by mangaluva. It has a huge mythology behind the Pandora gem but ultimately it brings all the characters together to end the Black Organization. It also has romance but it doesn't jump in the face. All in all it is very well written fic that takes in count all the plot twists that far. It's long but also completed.
Then there is a continuation fic for movie 13: Raven Chaser. The name is Fallout by The Silversage. It's unfortunately incomplete and probably will stay like that but it's really good. The chapters take turns with investigations on Conan/Kaito/Heiji+eventually Hakuba side and Satou/Takagi side. No romance. I sometimes read only Satou-Takagi chapters because Conan-Kaito fics are so common.
Then there is quite humorous fic A Snowy Meeting by angelwingsonline. It combined Magic Kaito special episode 6 with Movie 15: Quater of Silence and the aftermath of Kaito getting mixed to the events of the movie... I'm not sure about the plot drive but it's quite nice too.
Black Echo by DiscordianSamba had Heiji as BO member Paikaru. Like, he was a member even before Shinichi shrunk. This is really good fic with a lot of thought for Heiji's character. There is also another fic by the same author were Heiji loses his memories in an encounter with BO and is brainwashed into becoming Paikaru while the cast thinks him dead. That one takes place in future where Conan has taken the permanent antidote.
Forgotten King by Rikkamaru. One-Shot about possible future. Leaves space for speculation.
Peering Through the Cracks by Sgamer82. Yokomizo brothers investigating Haibara with the scant information they have. It returns to status-que but it's interesting to follow their thoughts and conclusions.
Snapshot by Thefinalkey. I'm not sure about this one... But it has an OC as Shinichi's older sister. Unlike one would assume, it's quite well written and the story built. It's still in progress but follows quite interestingly the events of the Conan Arc(this far) from another point of view.
The Tragedy of the Woman in Red Revised - Detective Conan Alternative by Serinox. As the title says: Red Woman case alternative, with Shinichi replacing Conan. It's good. Only warning though... There is a chapter where you might want to stop reading... read through it, you won't get disappointed.
These all were taken from my favourite story list at FF.net thus the stories are found from there. I have a bunch of other fics on the list too mut I think these are the most suitable ones. I hope this list helps.