I had opened a similar discussion. Engineermusic referred me to this one. I had the same issue (messaging apps crashing, so I turned off and on the phone, and then all the contacts were gone). This happened to me twice. I believe the contacts are actually gone before you turn it off. The second time it happened, I tried to see if the contacts were gone, but the Contacts app wouldn't open either. I also do no synch to ICloud. I restored to my last backup, which worked, but then they disappeared again a few hours later.
I tried to chat with apple online, but my phone is out of warranty, so they wanted $20. I made an appt with the apple store genius bar instead. They didn't charge for this. The guy was very nice and tried to help, but he hadn't heard of this (yet) and didn't know why it was happening.
I have iphone 4S with iOS 5.1.1.
I make periodic backups, but I don't synch to iCloud.
The first time was 2/24/2013 around 11pm (pacific time).
The second time was 2/25/2013 around 11am (pacific time).
Both times I was using iphone messaging and the wechat messaging app.
I think the perspective roaminggnome suggests is good. (i.e. consider the phone as portable storage, but make sure everything is saved somewhere else). Until now, I've thought it the other way around (i.e. the data is on the phone and I back it up somewhere else). But I think roaminggnome is correct. Once I get everything back up, I will try synching to their iCloud.
The scenario sullimom24 describes is the reason I don't synch. I'd heard of people that lost data and then automatically lost the same data on their backup as soon as they connect to itunes and it synchs. This basically rendered the backup useless. The Apple genius told me if I synch to iCloud, then I can log into iCloud and view, print, or save the contacts elsewhere. This could be a backup that the synch doesn't touch...
Also, I am going to try the "My Contacts Backup" app that Zoomer271 mentioned. Thanks for also describing how to use this to restore from the phone itself. Seems like less hassle than the other options.