I was having the same problem described here. 'Reset Warnings' did not solve it for me. Or any of the other suggestions. A few weeks back I reset the entire phone but the problem came right back.
After another round of getting a series of messages 'could not sync 49 apps' etc....the number changing each time from 12 up (I have 82), and never the same number, plus a 'phantom badge' would indicate in iTunes that I had apps to update. When I clicked into that window, it would say that all my apps were up to date.
Here's what did solve it (for the time being at least):
I UNclicked boxes that would sync music, movies and photos in iTunes, removing them all from my iPhone. I continued to get the message that apps did not sync. This time it was only one that did not sync.
In the process, I noticed that when I click 'sync with this iphone over wifi' in iTunes summary, i get a message telling me that if I do, ONE APP will be removed and all of its data. I disconnected, reconnected, went to my apps and clicked that app so it would sync the next time.
I then synced all over again. I did not get the message that an app did not sync. And yes, that one app's data was clear but the app is on my phone again.
I synced a final time, this time including music. (I did NOT sync any photos.) In doing so, I had .34 G of free space left.
NO MORE messages that something did not sync. NO MORE 'phantom' badge in iTunes saying that an app needed syncing, when none are in the queue and the window says all your apps are up to date.
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I have no idea what any of this means. Is it a space problem? Is it just a bug in iTunes? Is it an iPhoto problem? Since the forums I have read did not have a solution that worked for me, I posted here to see if it helps someone else... or even better: maybe the bug can get fixed.
p.s. I use an iPhone 4, 16 G, Mac OSX 10.7.4, iTunes up to date.