I have had both of these scopes (Leupold VX-R 3-9x40 and Zeiss Conquest 3-9x40). Both are nice scopes but of course there are some differences.
As far as glass goes I would say the Zeiss has a edge but it is not exactly an overwhelmingly one. The glass on the VX-R is what I would say between a VX-2 and VX-3. (Not a VX-II and VX-III stop confusing these models people! I know Leupold kept a similar name but the VX-III and VX-3 are not the same!)
Eye relief they are both sufficient amounts but the Zeiss of course is constant throughout changing the power. The Leupold doesn't change a lot and this makes no difference to me. Some people it does so something to consider.
When comparing the quality some of the comments on here are laughable at best. Leupold makes some very good quality scopes and the VX-R is one of them. I will take the turrets on the VX-R over then hunting turrets that come on the Zeiss any day of the week. I felt the Leupold had better positive clicks with both turrets being very good. The Zeiss turrets were not the worst I have seen but the top was very tight and the side was okay. The Leupold also does not have plastic turret caps either like the Zeiss.
Again both are nice scopes but at the end of the day I would find myself with the Leupold. Reason being is because of how sensitive the eye box is on the Zeiss when it is cranked up to 9 power. If you don't hold your head just at the right position along with the sun, moon, planets and stars lining up in the universe there is a bit of blur in the scope except for the very center of the picture. I found this to be unbearable to me. Some people apparently don't mind this because there are a lot of people that love these scopes. My buddy and I both do not like this scope for this very reason. The Leupold is very forgiving. I have a VX-3 now and will say that I have not been able to notice any difference at low light between the glass on it and the Conquest. I have a feeling that some, not all, that make the negative comments about the higher end Leupolds have never even had one to judge.