Where is time machine backup of applications and library?

I have had regular time machine backups of my system for the past year. I have recently wiped my system and have done a fresh reinstall of OSX 10.8. 
I now need to restore some applications and application settings but the Macintosh HD/Applications and Macintosh HD/Library only appear in the very first backup from a year ago. No other backup contains anything except for the "user" and "shared" folders.
Nothing on the iMac internal disk was excluded from Time Machine. Username and password are the same in the new install.
All my hair has fallen out and I am rolling around on the floor in agony.
Any ideas?

It's possible for those folders to be excluded without anything showing in the Time Machine preference pane.
Triple-click the line below to select it:
defaults read /Library/Preferences/com.apple.TimeMachine SkipSystemFiles
Copy the selected text to the Clipboard (command-C).
Launch the Terminal application in any of the following ways:
☞ Enter the first few letters of its name into a Spotlight search. Select it in the results (it should be at the top.)
☞ In the Finder, select Go ▹ Utilities from the menu bar, or press the key combination shift-command-U. The application is in the folder that opens.
☞ Open LaunchPad. Click Utilities, then Terminal in the icon grid.
Paste (command-V) into the Terminal window. Post the line(s) of output that appear below what you entered.

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