iTunes trying to sync every app I have on my Mac?
This might be because of the change of iTunes apps layout or the apps couldn't be determined 

Check here for more information 
https://discussions.apple.com/thread/3395256?start=210&amp;tstart=0

https://discussions.apple.com/thread/2744493?start=45&amp;tstart=0


  2enjoy
  Re: Sync Apps from iphone to itunes changes the apps layout
  Sep 14, 2012 10:00 PM (in response to CybermanSG)
  so who wants the real answer??  its very simple...  
  
  as mentioned, first of all TRANSFER PURCHASES from iphone to itunes. check the SYNC APPS check button. yes this will cause itunes to reorganise your folders (for now), however, then close itunes. you will get a window pop up asking if you want to apply the changes. Select YES. itunes will then close. now re-open itunes and PRESTO!  itunes will now show all of your apps as selected and they will all be in the same folders as in your iphone. you can now sync away without losing your personal folders...
  
  this was done on a iphone 4S running 5.1.1 on itunes 10.7.0.21
  hope that helps.. enjoy!