LS-6 block.
The rest of the differences are all up top, where it's important:
Cylinder heads with lighter valves (and really good ports).
Camshaft with extra lift / duration & reduced base circle.
Longer pushrods because of the reduced base circle.
Better springs to handle the extra lift.
LS6 Intake (obviously) is significantly better than the LS1 intake.
I think the LS6 block may have been used on the late f-bodies ('02's) when the LS6 intake was also used (as a running factory change). But without the rest of the parts (heads, cam, valves, pushrods, springs) it's really still an LS1 (cylinder heads & cam are the key to power).
'JustDreamin'
The LS6 block is better. The windows are larger which makes a difference high up in the RPMs, I forget what RPM it is exactly, but somewhere up past 6k or 7k the windows in the LS1 blocks do not flow enough air and problems start to develop. They made the windows larger in the LS6 block so that they could safely spin more RPM. 




