Hmm well now I'm really confused. iTunes has spent the past 2 hours with a dialogue window claiming that the iPhone has been restoring Music and Videos, but while it was doing that the iPhone itself showed no indication at all that any syncing or restoring was going on. Now that the dialogue window finally completed iTunes then went into a more familiar syncing mode (with the progress bar in the top status bar), and the iPhone had the rotating sync icon next to the wifi symbol. Not sure what has actually been going on over the past two hours?!
Well now the music and videos seem to be back on my iPhone, but still none of my applications. I've now done a restore from the backup I did earlier on before applying iOS 5 but I still don't have any of my apps on the phone?! If I go into the Apps tab of the iPhone screen in iTunes it isn't set to sync them (it was before I applied iOS 5), but if I change that to sync now I suspect it will simply load fresh installs onto my iPhone and won't have any of my saved data.
[Edit: Grrrrrrr!!!! I suspect that at some point in the recent past iTunes has randomly turned off syncing my apps and unfortunately I didn't think to check before I applied the update as I hadn't changed the setting myself
As a result I appear to have lost all my saved data for each and every app! So pissed off - this is the first iPhone update I have done where I have lost all this sort of stuff, and I was even being very careful to back it all up in the run up to iOS5 launch.]
[Edit 2: Phew! After resyncing my apps back to the iPhone it appears that the saved data was retained somewhere - at least for the apps I was most concerned about!]