With Configuration Manager 2012 came a new UI. It took some getting used to but I, for one, have come to like it over the old MMC interface. There is one frustration with it that I hear from customers or see them attempting to workaround all the time. ConfigMgr admins everywhere like to organize their applications, software updates, etc. into nice folders, for easy administration. The downside of this is that when they or some other co-worker goes looking for a given application, they can't figure out which folder it is in. Many folks ignore the search ability at the top of the UI window because it only searches the current folder, or root.
The solution is to look a little higher and to the left. Up there and hidden among all the icons is a little button called "All subfolders". If you are on applications, collections, software updates, and probably several other locations you should be able to find it. The trick is that it doesn't show up initially. You must click in the search box, then you will see it. Some quick screen shots below, since a picture is worth a thousand words.