How to make sure all apps are in the backup iTunes makes?

I did a restore today to my iPhone 4S and it seems not all apps were in the backup I manually made in iTunes before the restore. Now I'd like to know how to not run into the same problem in the future.

Okay I copied iTimelapse Pro app (one of the 150 missing ones) from the Time Capsule hard drive to my laptops hard drive and synced iTunes with iPhone and I can see all my timelapse projects in there! Have to check if really all data is retained and then continue. It's a lot of work to try remember which apps are missing but I think we have a solution here: all the data from the apps are in the backup from today, it's just the apps that got messed up because of iTunes corrupted the links.
Thank you very much KiltedTim! Wouldn't solve this without you.

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