I got a MacBook Pro that has a problem booting, or even seeing the hard drive. I have used the recovery console to install OS X onto a USB drive and have booted into that and can't actually see the internal disk at all.
If I boot to Recovery Mode and open Disk Utility I can see it fine in there, and can see the files on it. If I check the disk using the repair option it also verifies fine.
If I take the drive out and put it in a USB caddy I can pull off all the files just fine using HSFExplorer on a PC, and have backed up most to an external drive from the PC. I can't quite work out why the Mac won't boot though as according to Disk Utility it's fine, but from inside OS X it cannot be seen, and also booting off it gives a question mark.
Best Answer
The question mark means that it cannot find its boot partition. On any OS X drive, you are going to have several partitions. It might look something like:
Using this drive as an example, you can probably see what is on "Macintosh HD0" which is disk0s3. To boot, you need the "Apple_Boot" partition or disk0s4 partition.
You should be able to fix this by running the installer and having it repair the OS X installation.
Make sure you back up your files first (it sounds like you did).