Is there any special episode of Conan and Kindaichi working together?
As of current writing, there's no special episode/manga chapter featuring the crossover of Detective Conan and Kindaichi Case Files.

The only real crossover is the Nintendo 3DS game (as you already mentioned), called "Meitantei Conan &amp; Kindaichi Shounen no Jikenbo: Meguriau Futari no Meitantei" (or "Detective Conan and The Young Kindaichi Files: The Chance Meeting of the Two Great Detectives").

Other than the game, there's a collaboration between Weekly Shōnen Sunday (Detective Conan) and Weekly Shōnen Magazine (Kindaichi Case Files) to celebrate 50th anniversary of Sunday Magazine by publishing a twelve biweekly magazines consisting of chapters from both series (full list of the chapters can be read here (in Japanese)). It's only a collection of chapters from both series, not a crossover though.

Other than that, there are canned coffee featuring both characters, and a Game of Life featuring both series.

Reference:


Ho-Ling's Blogspot
Wikipedia article on The Kindaichi Case Files