So this happened to me a SECOND time three days ago. Interestingly, it happened when I was playing with Windows Live Search features while the phone was signaling low battery power. Now, I'm not 100% sure if the low battery situation was part of the problem but I can say that it was almost immediately after this that I noticed the corruption. Once again, the programs tied to my SD card weren't working and their icons were "blank", plus all of the files and folders were gone but replaced by "gibberish" folders. Sadly, my BACKUP on the SD card also disappeared so I couldn't do a quick restore like I did last time. So I resigned myself to re-install those SD card items when I got home in a few days.
However, last night I encountered an interesting development. I decided to download Picsel Browser directly to my SD card and re-install it there (one of the SD card victims). I finished the download but then had to go do something and didn't get back to my Touch for a couple of hours. When I went back to the phone and looked up the file using the file explorer, I noticed that all of the folders and files that went missing earlier had REAPPEARED. Despite the two or three "gibberish" folders remaining on the card, everything seems to be back to the way it was before the glitch. Weird.
Well, to say the least, I let out a big sigh of relief. I don't know what brought THIS about, but I'll take it.
Regardless, my policy now is to make sure I keep a copy of the backup on my PC just in case.
But now one has to wonder: are SD card issues (like the 6700's BSOD and this corruption problem) even more likely to be related to the SD card slot POWER? Keep in mind that NOTHING on the Touch itself seems to be affected by this issue.