Usually, it depends on the application. With GPE, I think it works fine, so long as you copy the /home/user/.gpe directory to your MMC card and then move it back after you re-flash.

I believe (don't quote me on this) that the Backup utility on the 770 works between scirocco and gregale, so doing a Backup before you reflash and then restoring that backup after you reflash will allow you to keep your bookmarks and other settings (including Maemo Mapper's settings).

I would back up your entire /home/user directory, though, just in case. That directory contains all of your user settings, and (theoretically) you could just copy your old /home/user directory over your new /home/user directory and get all your settings back. I wouldn't actually go that far, though, because some data formats may have changed. Just keep a backup of /home/user handy, so you can selectively try restoring settings on an application-by-application basis. It never hurts to back up files - if you break something trying to restore it, you can always re-flash and try again.

Good luck!