After installing Mac OS X 10.7 Lion I noticed folders were missing. For me the main issue was that the Library folder in my user account seemed to have vanished. As this folder holds nearly all the data that applications save without asking such as mail, preferences, calendars and virtual disks it was important to have an easy way to manage it, especially as I wanted to exclude the Steam folder located there in Time Machine.
Simply launch Terminal from your applications/utilities folder and type
chflags nohidden ~/Library