I backed up to itunes but it didn't transfer to my new iphone I did a backup of my iPhone 4 to iTunes in anticipation of getting a new iPhone 5S. 

When I did the restore to my new iPhone after I got the new phone, it didn't give me the latest data that was on the old phone. 

What happened? Is that data gone forever since I no longer have that old phone?
As long as you have the data backed up it should still be available. That being said, it depends on the amount of data you decided to back up. Also make sure to use the same iCloud ID since you might have started to use the iCloud for backups and not you PC.

Both Backup and Restore procedures for iCloud and iTunes is listed on Apple Support website.