Hi, I would have to disagree with those who say the answer to this question is 
a matter of opinion. The question asked specifically about the best means of 
backing up. Not the easiest or the most convenient, but the best. There is in 
my view only one answer to the question when it's phrased this way, and it is 
this. The best way to back up your device is with an encrypted backup in 
iTunes. Here's why.
An encrypted backup is the only way of backing up passwords and other sensitive 
data. If you restore from an iCloud backup and log into apps like Skype, or 
similar apps requiring you to sign in, you'll need to sign in again. Encrypt 
your backup on iTunes and you avoid this hassle.
The point has already been made in this thread about the desirability of an 
iTunes backup if you keep old copies of apps for accessibility reasons. But 
there's more to it. Your apps are not backed up to iCloud at all, and when you 
restore using this method, the latest version of the app is downloaded. But 
what if you have an app that has been pulled from the store, either by Apple, 
or by the developer because they no longer wish to support it? The answer is, 
restore from iCloud and you're just out of luck. You've lost that app for good.
iCloud backups don't back up your music. If all your music comes from the 
iTunes Store, or you have iTunes Match, this is no problem at all, but it's a 
consideration if you spent lots of time initially syncing music from your 
computer. You can of course sync with your computer after restoring from an 
iCloud backup, but if you have to do that, you may as well do the whole thing 
from iTunes and enjoy the benefits.
Personally, I use both methods just for safety's sake. My devices back up to 
iCloud every night, but when I connect to iTunes, I manually initiate an 
encrypted backup. That way, if I'm travelling without my computer and need to 
get up and running again, I can, but iTunes is my first restore preference for 
the above reasons. So it's certainly possible to use both.
No doubt iCloud is the most convenient from a set it and forget it point of 
view.

Jonathan Mosen
Mosen Consulting
Blindness technology eBooks, tutorials and training
http://Mosen.org

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