The Soul Stealer by Nathan Alderman is a due South & X-Files crossover. When a federal witness mysteriously dies in Vecchio’s and Fraser's custody, Mulder and Scully travel to Chicago to investigate.
North West by equestrianstatue and omnishambles is a canon divergence where Vecchio and Fraser get to Fraser’s cabin up north and work on repairing it together.
Lair of the White Wolf by ButterflyGhost is a case!fic with an ensemble of canon characters and OCs.
The High Iron Fist by Shadow2Serenity is a case!fic with an autistic OC and is written by an author who is autistic.
Man in Red by A. J. Dannehl is a crack!fic due South & Men in Black crossover that references Juliet is Bleeding, Victoria’s Secret, and Burning Down the House.
A Single Bullet by crosscountry07 is episode-related for Victoria’s Secret and Letting Go, and there is also a fanmix that goes with this fic.
Be a Conduit by clevermanka is a Burning Down the House missing scene with Welsh and Vecchio.
Credit Where Credit is Due by mizface has Frannie and Elaine discussing life choices.
Then there’s dS_Tiff, author of so much dS gen that I’m not even going to attempt to rec individual fics. Check out her dS fic list on AO3. (Note: Out of 42 fics for dS, 39 are gen, 2 are slash co-written with Vic32, and one is het.)