Epilogue: I managed to recover all of my data!
I'm also rethinking my backup strategy; I think I am going to go for a distributed backup on each workstation/server to an external hard drive to eliminate single-point-of-failure - I might also continue to keep the backup to the server as well, if I can rig the workstations to do the dual-backup scheme.
Where did my data go? Well, I think I actually caused the worst of it on the one drive that held all my media; I think at some point I performed an fsck on the web interface, and it was taking a while and I didn't know if anything was happening - in my haste, worry, fear, confusion, doubt, anger, etc - I probably reset the system, leaving the file system on that drive in a very weird state. Well, for S&G, I decided to run a full fsck (on both drive), be patient, and wait. At the console, a combo of ps and top proved that fsck was doing work, so I just let it sit. When it came back, all my files were sitting in lost+found. The other drive where the backups were stored didn't have any issues (fsck found no problems).
Since the drive that my backups were going to had a SMART failure on boot, I decided the other drive (where the media is stored) couldn't be too far behind. I had purchases a second set of 400 GB drives, with the intention of building a second server, but I never got around to it (which was a good thing). I copied all the data to the second pair of drives, installed them, and all was good.
In addition, I added heat-sink/fan combos to each drive, plus an extra case ventilation fan (a largish PCI slot fan). While testing fan output and drive temperature, I noticed that the PSU fan was not turning fast; I ended up pulling it out and re-lubing it - I'll probably end up replacing it in the near future (might replace the entire PSU). After that, the temperature of the drives seemed better than before; they're running now at about 37C, before (the old drives) they were around 45C.
I was pretty worried there; ultimately a night's sleep and some food made the next day clearer, and allowed me to see some mistakes I had made previously. One of the interesting ones were setting some jumpers on the new pair of drives - I had bought these drives fairly cheap from computergeeks.com ($40.00 for a 400 GB PATA drive), but they kept showing up as a 32 GB drive when I installed them. It turns out that there were two different settings for the jumpers, one set for "full drive capacity", and a separate set for "32 GB cutoff"; in my haste and worry, I had selected the wrong set (and thought that I had been ripped off!). I don't know what the "cutoff" set is for, but once I had some sleep and looked it over in the morning, I saw my mistake. I ended up taking back the Serial ATA interface and drive I had bought (saving me $100.00).
I am soooo glad that I won't have to re-upload all of that data back onto that media drive. In the meantime it was an interesting lesson all the way around, in a lot of areas that I hadn't thought about. The biggest two would have to be run fsck more often, and to keep an eye on the SMART status messages, neither of which I was doing as well as I should have.
Finally, I still recommend FreeNAS as a great way to build a NAS box on the cheap.