The apps are stored on the phone rather than the memory card, so they get wiped off when any major updates take place. If they are from the Android Market, you can download them again free of charge. Still a bit of a pain, I know, but they shouldn't be gone for good. You could even see it as an opportunity to weed out some of the apps you don't really need but downloaded from the market because you were feeling 'app happy' with your new phone...:smileyhappy:
I think you'll be able to store the apps on the memory card once we get Android 2.1.
