So a few months ago my 60 gig PlayStation 3 (with the all coveted PlayStation 2 backwards compatibility) decided that its blu-ray eye would stop working. I sent the unit for repair, etc. etc. which was a relatively pain free process (the cost not as much). Luckily they were able to repair my unit and send the same one back. Now, the Sony representatives on the phone told me that all I had to do was backup my hard drive using the Backup/Restore utility and all my data would be preserved. However, what the representative forgot to tell me was that the backup utility
does not backup or restore any PS1 or PS2 save data.
So shock and awe, when I finally received and restored my machine I had lost all my progress in Persona 4 (the game I was playing at the time) plus several older games (those massive GTA saves). Now I don't blame Sony per say, but I would like to advise everyone with a backwards compatible PS3 to backup your older game save data to a memory stick, external drive or even (if you're lucky enough) PlayStation 3 Memory Card Adaptor (see image). The useless device at launch (because you could only read at the time) was firmware upgraded ages ago to allow writing to memory cards. Luckily I kept one PS2 memory card with some legacy saves (Final Fantasy series and Metal Gear series) so I wasn't completely screwed. But still, all the work in Persona gone.
So I advise everyone who has a backwards compatible PS3 (or anyone with PS2 or PSOne save data on their PS3) to remember to do backups of their save data to other media. The allmighty Backup/Restore Utility does the best job it can for the PS3 but isn't perfect... and now you know. And knowing is half the battle.