I just looked at my Utilities folder, and nothing seems to be missing, except that I don't have the Java app.
Press CMD+2 and then CMD+1 again, and it should be sorted alright.
To the other vague question.
Gravity maybe.
You can use Disk Inventory X (www.derlien.com) to scan your HDD for all the Gigabytes and where they have gone.
Also have a look at Activity Monitor.
Repaired Permissions?
Restarted?
Installed bunch of software?