Apps Backup/Recovery

I purchased a new iPhone, did a backup of my old phone on the new iTunes, when I did the restore to the new phone the apps didn't all transfer over. Have I lost all the data? I keep all my store cards and business cards on two apps. Have I lost it all?

How do I back up my app data now? What if I loose my phone again. Oh and I do NOT want to use iCloud. It is not secure.

Can I restore to an older version of iTunes to get the app option back?