I don't know what it is but generally funguses and such are from too much shade and too much dampness.

You can't do much about the shade but you can help the dampness by pruning such that the branches are 'airy' and allow for a lot of air circulation in the tree between branches.

When and if you water they probably don't need watering any more at their size based on the pears you show.

Rust.
We don't have that around here, so I suggest you consult your county's Extension Service office.

Use this map
http://www.csrees.usda.gov/Extension/

Here is a link that might be useful: locate your County's Extension Service office

Thanks jean001a, after a quick google, it does appear to be rust. The odd (but good) thing is it only affected a few pears on the one tree and it never spread to the leaves or other pears on the tree. I sprayed all my trees with a sulfur spray while they were dormant and once again right after the fruit formed, wondering if that kept the rust at bay?
AgroCoders, I was thinking the same thing, the Kieffer that was affected is in more shade then my other pears and it might be why it got hit first, thankfully it was not that bad and only affected a few pears.
Thanks for the help guys,
Matt