lost library

Do you see two iTunes folders on your computer, one being the old one? If you do, start iTunes with the alt key trick and switch back to the old library. The question will then be did iTunes move or copy your music files when you added them to the new library.

Sounds like you have an incomplete library folder. Read below on what makes a complete iTunes library:

What are the iTunes library files? - http://support.apple.com/kb/HT1660

More on iTunes library files and what they do - http://en.wikipedia.org/wiki/ITunes#Media_management

What are all those iTunes files? - http://www.macworld.com/article/139974/2009/04/itunes_files.html

iTunes 9 [and later]: Understanding iTunes Media Organization - http://support.apple.com/kb/ht3847

Image of iTunes folder structure Dec. 2011 - https://discussions.apple.com/thread/3547807?answerId=16923545022#16923545022
see also:
Image of folder structure and explanation of different iTunes versions (turingtest2 post) - https://discussions.apple.com/thread/2741246?answerId=13025536022#13025536022 and https://discussions.apple.com/thread/3700206?answerId=17457605022#17457605022

A device is designed to sync to one library at a time. When you hook it to the new library it sees it as a new library and wants to make all the content on the phone identical to the library to which you are syncing it. If you can somehow find that old library.itl file that belongs in the old itunes folder you can regain your old library. It it is gone then you're stuck with building a new library and syncing to that.

I have no apps so I cannot try this but what happens if you drag the folder with the apps to the new library you created? Does it add them the way it would media?

https://discussions.apple.com/thread/4121695?answerId=18968829022#18968829022 - make a smart playlist to show music purchased from iTunes Store