I just sort it by vehicle with a log sheet of work performed, mileage, date, etc.. I dont keep many recipts anymore - only long enough just in case i need to return something soon ( dont wanna know how much I spend on these cars .. ).
I usually own 7-9 cars at a time, and work on customers and family's cars .. so lots of cars to keep track of.
I transferred all of my paperwork to a PC and would keep track of it there until the hard drive failed and I lost my records .. I dont bother with that anymore.