I'm not getting
root either. There's a new option in CM9 under Settings -> Developer Options -> Root Access that allows you to specify whether apps and/or adb get to use root.
I tried all options (also with USB debugging on/off) and rebooting but nothing seemed to make a difference.
btw, the adb shell has full device access no matter how you configure the Root Access option. I guess if Root Access was turned off for adb, you shouldn't even be able to cd into /data/data etc.
Titanium Backup says it tried to call /system/xbin/su unsuccessfully.
As for
gapps, I successfully installed the most recent ICS version from
here by manually extracting the system folder to my /sd-ext and then symlinking the contents of each folder into the corresponding directories in /system. You just need to cd to each of the 4 folders (tts files are already the same) and do it like this:
cd /system/app
find /sd-ext/system/app -maxdepth 1 -type f -exec ln -s {} \;
In /system/app you should also
rm Gallery2.* Provision.* QuickSearchBox.*
This may not be a suitable solution for everyone because you can't assume that an sd card is present (+ the ext-partition) but it'll do until /system loses a few pounds. I see some useless 10 MB in /system/media/video for an instance and maybe some odex files can go or some apks can be loaded off to /data/app.