After countless hours this past weekend with this same problem (iTunes stuck on "waiting for changes to be applied..." I finally have resolved it without having to completely rebuild my iTunes library (and losing my metadata in the process). For background, I updated my iPhone 4s while I was traveling, and when I returned home, I was no longer to update music in iTunes (it would hang).
The problem, it seems, is related to several factors:
1) you have enabled "Find My iPhone" in the iCloud settings on your iPhone
2) you have initiated a download of music through iTunes on your iPhone, and the downloads have not completed
3) you have a corrupted Voice Memo, causing duplication on each sync
Here's what I ended up doing:
on your iPhone / iPod / iOS device:
1) disabled "Find My iPhone" on the iCloud settings of my iPhone
2) gone to the "Downloads" section of the iPhone "iTunes" app and deleted every in-progress download
3) go to Voice Memos app and see if there are recordings in the list that may have been duplicated
you can also check the "Voice Memos" playlist on your iTunes library
- delete any duplicate Voice Memos; if some memos are gray and can't be deleted see below
4) do a cold reboot (hold down top bottom, power off, then on again) but do not dock your iPhone yet
on your iTunes:
5) change your iTunes -> Devices preference to "Prevent iPods, iPhones, iPads from syncing automatically"
you can now dock / connect your iPhone to iTunes
6) select "Manually manage music and videos" in the Summary tab for your iPhone within iTunes
7) go to the Music tab for your iPhone within iTunes
- you may see a list of music at the bottom called "manually added music"
if present, select all items in this list and Delete to remove them
8) uncheck "Sync Music" at the top of the Music tab and "Apply"
- this will remove all music from your iPhone
9) if the iTunes sync completes properly, perform a Local Backup of your iPhone (you may need this later)
10) re-enable "Sync Music" but uncheck "Voice Memos" and "Apply"
- if this fails, you have a corrupted memo - see below
11) if this sync completes, change your iTunes -> Devices preference to disable "Prevent iPods, iPhones, iPads from syncing automatically"
possibly optional steps needed:
a) make sure you have a backup of all of your Voice Memos (check iTunes)
you may want to copy off these files and then remove them from iTunes, especially if there are duplicates
b) if your Voice Memos database is corrupted, you may need to clear out the iPhone internal database
there are third party utilities (I used "iPhone Disk") that let you access the directory even on a non-jailbroken phone
b) remove all files from the "Recordings" directory
c) cold-boot your iPhone
d) repeat steps above
Again, this sounds painful (it was!) but after many tries, this is what finally allowed my iPhone 4s with iOS 7 to once again sync properly with iTunes 11.1. This process will preserve your iPhone settings, voicemails, Messages, etc. And, it will let you retain your iTunes library without rebuilding.
