Perhaps the biggest geographical advantage that the Western Europeans had was the fact that they were a part of the huge continent of Eurasia.  This continental mass was home to a number of epidemic diseases that were not present in places like the Americas.  When the Europeans reached places like the Americas, the diseases that they carried with them killed millions of the natives.  The natives had no resistance to the diseases and huge percentages of them were killed by exposure to them.

In this way, being geographically connected to a large area with a huge population exposed Europeans to diseases that the Americans had not been exposed to.  This was a major advantage for the Europeans.