It took me ages to connect the Astonishing X-Men arc, Ghost Box (and the related Ghost Boxes mini) with Ghost Box Records, the hauntology label. Added a whole other layer, once that clicked.
As West Coast Avengers was the only place I'd ever encountered "How's tricks?" and as soon as a character says it, they apologize for it being impolite, I just assumed for ages it was something dirty.
And, I still don't know who Reg and Daphne are in an issue of Wolverine where he visited Muir Island.
Any allusions or references that mystified you for years, or to this day?