'Tis all fixed now. Users around the globe have blogged, and tweeted, and all that stuff about how it's working again. It was just a calendar bug in the end. Sony have apologised, and they've given us info to get any lost trophys back.
Just insert the affected game while you're online, so that you get the trophy bar back up for the game, then quit, then sync the trophys via your online profile and they should return. It hasn't worked for everyone, some people see the trophy bar and some don't, but regardless you'll get the trophys back, you just might not be able to see them, but they'll be there. If you compare trophys with a friend, you'll see you still have them. I haven't tried it, but I trust Sony on this.
So all is well. It was only a day without PS3, I'd like to have seen the reactions if it was a month.