Librarian Heather Riley of the Urbana Free Library in Illinois has put together an excellent gateway to middle grade mystery novels, with sections for classics, historical, realistic, action/adventure, and fantasy/paranormal. I'm pleased to see The Mysterious Benedict Society included -- I loved that book as much as my kids did.
Thank you, Heather! But I think you accidentally left out Daniel Pinkwater's Snarkout books, in which a bunch of kids (all boys and one girl, typical Pinkwater but we love him anyway) work with the Sherlockian "Osgood Sigerson" to solve bizarre mysteries involving avocados and other things. (By the way, the name Sigerson is Holmes's pseudonym in "The Adventure of the Empty House," a 1903 short story by Arthur Conan Doyle; it is also the name of Holmes's "smarter brother" in the 1975 Gene Wilder film.)