Thanks very much Kevin, using the %Name%_%n% added the iteration number to the name and now I get all of the outputs and not just the last one.
I like the thought of the second suggestion using the Python code but alas my Python coding is not very strong. This is my situation: Currently I have a folder and it contains a separate file geodatabase for each of the KMLs I created in GE and each of those file geodatabases has the correct name from the KML. Inside each file geodatabase is a file geodatabase feature dataset and inside that dataset is the Placemarks_polygon feature class for that respective geodatabase. So each file geodatabase has the correct name, but then the feature class inside each of the over 100 geodatabases has the same Placemarks_polygon name and so when I run the model I get Placemarks_polygon_1, etc. but then I have to rename each of those outputs to correspond to the name of the geodatabase, redundant and I'm sure un-needed using ArcGIS.
So, I was using ModelBuilder to iterate through these feature classes, re-projecting them all to my UTM zone but I don't have the knowledge to get it done as efficiently as I know it probably can be. The final product I would like is a single feature class or dataset that contains each of the over 100 feature classes and each one to have the appropriate name. I am creating a feature class of building footprints that have the owners name as the name of the feature class. As I have over 100 buildings I want them all contained in a single feature class with owners listed.
Sorry for the length of the post but I am trying to add as much detail to get the best help possible, thanks.