Experimenting with the new cyanogenmod builds for Android 4.3 (cm-10.2) resulted in a disaster: my phone was setup for encryption, and the updater messed up the usb storage such that the phone wouldn't recognise the in-built sdcard on the Nexus S anymore. I tried several things: factory reset, formatting via the clockworkmod recovery, etc., to no avail. The recovery wouldn't recognize the /sdcard partition, too.
Good thing I had a backup, so I wasn't worried too much.
I could use adb when CWM recovery was booted, to navigate around. Using fdisk, I could see the /sdcard partition was intact, but wouldn't get recognized by either CWM or the kernel. I deleted the partition, and created a new one with the same parameters. Also used the opportunity to try out ext4 instead of the default fat. CWM still wouldn't recognize / mount this partition, but the android kernel does recognize it. However, mounting the card as USB storage still doesn't work.
So I've now fallen back to using adb + rsync as my backup solution: usb-tether the phone to the laptop, note the IP addr the laptop got, and then from an adb shell, just issue
'rsync -av /sdcard/ user@laptop-ip:/path/to/backup/'
This is working fine. adb push/pull also work quite well, and I don't really miss the 'mount as usb storage' functionality much. I'll however try fixing this issue, since encryption isn't working as well -- so the key would be to ensure CWM recovery identifying the partition. I'm guessing if that works fine, the remaining bits would be fine too (mounting usb storage, encrypting it, etc.)
I use GOBackup from the Play store to backup apps+data. oandbackup from the fdroid store looks nice, but crashes a lot. It's being constantly updated, though, so it has promise to become a nice backup app.