I also lost all of my contacts and messages. When I plugged my iPhone 3gs into my computer to try to restore it with my last backup, it synced and overwrote the last backup. Figures. Guess they're gone forever now.
The problem for me was that some time in the past year I had changed the e-mail address for my Apple ID, but it had not changed in my iCloud settings. So, it has been trying to connect to the wrong e-mail address this whole time, meaning it hasn't actually been backing up anything. Luckily, most of my contacts were backed up on my computer. As for the messages, I don't think those will be coming back.