Last edit
Summary: Patience is key.
Added:
> Against all odds and after waiting what looks like an hour, the message has changed from "Waiting for changes to be applied" to "Copying photo 453 of 3271!" Patience is key. I also checked the "include videos" checkbox in the Photos section because I wanted the videos as wall and because I felt that maybe I should change something in order to trigger the synchronization again as it was quietly failing before. Perhaps that wasn't necessary and the simple reboot and the extra patience after that was enough.
> For the record and in case anybody stumbles over this page in the coming years: I'm using Mac OS X 10.6.8 and a first generation iPad and I'm synchronizing more than 20'000 photos which take around 15GB.
I’m having the stupid Waiting for changes to be applied when synchronizing my iPad. Again.
Here’s a potential cause:
We have multiple iPhoto libraries on this computer. My default iPhoto library is “Alex iPhoto Library” but today I started to synchronize the iPad and iTunes told me that it would wipe all the photos on my iPad but that all the photos on my iPad would be unaffected. Huh!? I decided to not synchronize photos and proceeded. After the sync I verified that the checkbox for synchronizing photos was no longer checked. I started iPhoto and realized that it started with “Claudia iPhoto Library”. I switched the library: quit iPhoto and press Alt while starting it again – what an idiot user interface! Discoverability? 0%! Then I went back to iTunes, checked the sync photo checkbox again and started the synchronization again. It has been stuck for seven minutes “waiting for changes to be applied.”
Thrice cursed bug of a castrated wolf howling at street lights! 
I’ll following my own advice I gave myself three weeks ago: Just restore the stupid thing.
I hate doing this.
I totally expect there to be problems with all the apps containing downloadable content such as all the tables for my beloved Pinball Arcade.
Update: The next day, the reset is complete. A message greets me saying that over 6000 objects could not be synchronized and that more info would be available in iTunes. No such info is available in iTunes, of course. 
I quickly try to sync the iPad again, and guess what? “Waiting for changes to be applied!” I wait some more. And suddenly: “Copying photo 1 of 12695!” Wow, perhaps this will work after all! After a while a message tells that over 3000 objects could not be synchronized and that more info would be available in iTunes. No such info is available in iTunes, of course. But the number has decreased. I feel encouraged.
I quickly try to sync the iPad again but no more progress is made. The photos synchronized end sometime in 2011. Will try to reboot the iPad and retry. Time passes. “Waiting for changes to be applied.” This makes me so tired.
Against all odds and after waiting what looks like an hour, the message has changed from “Waiting for changes to be applied” to “Copying photo 453 of 3271!” Patience is key. I also checked the “include videos” checkbox in the Photos section because I wanted the videos as wall and because I felt that maybe I should change something in order to trigger the synchronization again as it was quietly failing before. Perhaps that wasn’t necessary and the simple reboot and the extra patience after that was enough.
For the record and in case anybody stumbles over this page in the coming years: I’m using Mac OS X 10.6.8 and a first generation iPad and I’m synchronizing more than 20’000 photos which take around 15GB.