Maybe all the older ones, Joopin, but not the newer ones. Mine came with the 44 rear (at my request). I don't know when they started adding that option.
He asked about the YJs specifically though? I know some TJs came with a "dana 44"... I'm pretty sure none of the YJs, unless you know something I don't.
Just to add to the confusion, Dana 35s between 87 and 89 were non-c-clip axles where 90 and up are the c-clip D35. The non-c-clips have a tapered axle shaft and 10" drums, as opposed to the 9" drums that 90+ YJ D35's have.