Ferrari 330 P4 came with a roof and without. I believe the one in GT5 is the 'barchetta' version. XJ13 I don't think ever had a roof. MKIV,GT40 and 2D have roofs.
Recon mentioned the Cobra. The Premium version is the Shelby Cobra which has Left Hand drive (it's American) and only appears with it's roof down, but it's a convertable. The AC Cobra (right hand drive british version) is Standard and has it's roof perminantley up.